Index – _

__add__() (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.utility.CSI_Sequence method) __ATTEN_ENUM__ (class in pyrosetta.rosetta.core.scoring.sc) __bool__() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) __call__() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (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.OptionCollection 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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) __contains__() (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) __delattr__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.TracerPriority attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.mpi.listener_tags attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.AA attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.Ancestor attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomProperty attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) (pyrosetta.rosetta.core.chemical.BondConjugability attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.GreekDistance attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBDefType attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) (pyrosetta.rosetta.protocols.helical_bundle.DoFType attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PertType attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.StatsType attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.Direction attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.Partner attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TrialResult attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.OptionTypes attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) __dir__() (pyrosetta.CD method) (pyrosetta.EnergyMethod method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerManager method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __div__() (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) __dummy__() (in module pyrosetta.rosetta.utility) __eq__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) __eq__() (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult 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.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __format__() (pyrosetta.CD method) (pyrosetta.EnergyMethod method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerManager method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __ge__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.TracerPriority attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.mpi.listener_tags attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.AA attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.Ancestor attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomProperty attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) (pyrosetta.rosetta.core.chemical.BondConjugability attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.GreekDistance attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBDefType attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) (pyrosetta.rosetta.protocols.helical_bundle.DoFType attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PertType attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.StatsType attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.Direction attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.Partner attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TrialResult attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.OptionTypes attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) __getattribute__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.TracerPriority attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.mpi.listener_tags attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.AA attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.Ancestor attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomProperty attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) (pyrosetta.rosetta.core.chemical.BondConjugability attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.GreekDistance attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBDefType attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) (pyrosetta.rosetta.protocols.helical_bundle.DoFType attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PertType attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.StatsType attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.Direction attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.Partner attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TrialResult attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.OptionTypes attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) __getitem__() (in module pyrosetta.method_bindings.pose) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) __getstate__() (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __gt__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.TracerPriority attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.mpi.listener_tags attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.AA attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.Ancestor attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomProperty attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) (pyrosetta.rosetta.core.chemical.BondConjugability attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.GreekDistance attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBDefType attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) (pyrosetta.rosetta.protocols.helical_bundle.DoFType attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PertType attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.StatsType attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.Direction attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.Partner attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TrialResult attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.OptionTypes attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) __hash__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) __hash__() (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __iadd__() (in module pyrosetta.method_bindings.pose) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) __idiv__() (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) __imul__() (in module pyrosetta.method_bindings.pose) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) __init__ (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) __init__() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __init_subclass__() (pyrosetta.CD method) (pyrosetta.EnergyMethod method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerManager method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __instantiate__() (in module pyrosetta.rosetta.core.pack.dunbrack) __int__() (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __isub__() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) __iter__() (in module pyrosetta.method_bindings.pose) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) __le__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.TracerPriority attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.mpi.listener_tags attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.AA attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.Ancestor attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomProperty attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) (pyrosetta.rosetta.core.chemical.BondConjugability attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.GreekDistance attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBDefType attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) (pyrosetta.rosetta.protocols.helical_bundle.DoFType attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PertType attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.StatsType attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.Direction attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.Partner attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TrialResult attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.OptionTypes attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute)

__len__() (in module pyrosetta.method_bindings.pose) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) __lt__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.TracerPriority attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.mpi.listener_tags attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.AA attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.Ancestor attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomProperty attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) (pyrosetta.rosetta.core.chemical.BondConjugability attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.GreekDistance attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBDefType attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) (pyrosetta.rosetta.protocols.helical_bundle.DoFType attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PertType attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.StatsType attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.Direction attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.Partner attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TrialResult attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.OptionTypes attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) __mul__() (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb 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) __ne__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) __ne__() (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult 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.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __new__() (pyrosetta.CD method) (pyrosetta.EnergyMethod method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerManager method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __reduce__() (pyrosetta.CD method) (pyrosetta.EnergyMethod method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerManager method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __reduce_ex__() (pyrosetta.CD method) (pyrosetta.EnergyMethod method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerManager method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __repr__ (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) __repr__() (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __setattr__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Cstring attribute) (pyrosetta.rosetta.ObjexxFCL.Dimension attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub attribute) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum attribute) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Fstring attribute) (pyrosetta.rosetta.ObjexxFCL.Fsubstring attribute) (pyrosetta.rosetta.ObjexxFCL.IndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.TracerPriority attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.mpi.listener_tags attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.JobOptions attribute) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManager attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.AA attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.Ancestor attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.Atom attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomProperties attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomProperty attribute) (pyrosetta.rosetta.core.chemical.AtomType attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.Bond attribute) (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) (pyrosetta.rosetta.core.chemical.BondConjugability attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.GreekDistance attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Orbital attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperties attribute) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.ResidueType attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformer attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.Atom attribute) (pyrosetta.rosetta.core.conformation.Conformation attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.Residue attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition attribute) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation attribute) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation attribute) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.AnnotatedFragData attribute) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet attribute) (pyrosetta.rosetta.core.fragment.FragSet attribute) (pyrosetta.rosetta.core.fragment.Frame attribute) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD attribute) (pyrosetta.rosetta.core.fragment.JumpingFrame attribute) (pyrosetta.rosetta.core.fragment.NonContinuousFrame attribute) (pyrosetta.rosetta.core.fragment.SecondaryStructure attribute) (pyrosetta.rosetta.core.fragment.SingleResidueFragData attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore attribute) (pyrosetta.rosetta.core.id.AtomID attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_ID attribute) (pyrosetta.rosetta.core.id.DOF_ID_Range attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.id.JumpID attribute) (pyrosetta.rosetta.core.id.NamedAtomID attribute) (pyrosetta.rosetta.core.id.NamedStubID attribute) (pyrosetta.rosetta.core.id.StubID attribute) (pyrosetta.rosetta.core.id.TorsionID attribute) (pyrosetta.rosetta.core.id.TorsionID_Range attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.AtomInformation attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique attribute) (pyrosetta.rosetta.core.io.LinkInformation attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.StructFileRep attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.Edge attribute) (pyrosetta.rosetta.core.kinematics.FoldTree attribute) (pyrosetta.rosetta.core.kinematics.Jump attribute) (pyrosetta.rosetta.core.kinematics.MoveMap attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.Stub attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.Particle attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.PackerTask attribute) (pyrosetta.rosetta.core.pack.task.PackerTask_ attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CSA attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy attribute) (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.DipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.EMapVector attribute) (pyrosetta.rosetta.core.scoring.Energies attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.Hairpin attribute) (pyrosetta.rosetta.core.scoring.Helices attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunction attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.Strands attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing attribute) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func attribute) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc attribute) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc attribute) (pyrosetta.rosetta.core.scoring.func.ConstantFunc attribute) (pyrosetta.rosetta.core.scoring.func.EtableFunc attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.Func attribute) (pyrosetta.rosetta.core.scoring.func.GaussianFunc attribute) (pyrosetta.rosetta.core.scoring.func.KarplusFunc attribute) (pyrosetta.rosetta.core.scoring.func.MixtureFunc attribute) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.SoedingFunc attribute) (pyrosetta.rosetta.core.scoring.func.USOGFunc attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet attribute) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.loop_graph.Loop attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ attribute) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax attribute) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover attribute) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Segment attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.DnaDesignDef attribute) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover attribute) (pyrosetta.rosetta.protocols.docking.DockSetupMover attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingProtocol attribute) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover attribute) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.TemperedDocking attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBDefType attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.FragLib attribute) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragment attribute) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) (pyrosetta.rosetta.protocols.helical_bundle.DoFType attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PertType attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.InnerJob attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.Job attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.Batch attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SameStrand attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.Loop attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.Loops attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileIO attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.AAProb attribute) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField attribute) (pyrosetta.rosetta.protocols.mean_field.MeanField attribute) (pyrosetta.rosetta.protocols.mean_field.ResHashMap attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.mean_field.RotMatrix attribute) (pyrosetta.rosetta.protocols.mean_field.RotProb attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CycleMover attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) (pyrosetta.rosetta.protocols.moves.RandomMover attribute) (pyrosetta.rosetta.protocols.moves.RepeatMover attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.SequenceMover attribute) (pyrosetta.rosetta.protocols.moves.StatsType attribute) (pyrosetta.rosetta.protocols.moves.TrialMover attribute) (pyrosetta.rosetta.protocols.moves.UDPSocketClient attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraint attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer attribute) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.Direction attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.Partner attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol attribute) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 attribute) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 attribute) (pyrosetta.rosetta.protocols.sewing.Assembly attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly attribute) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly attribute) (pyrosetta.rosetta.protocols.sewing.HashEdge attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ModelNode attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers attribute) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover attribute) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy attribute) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ShearMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmallMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TrialResult attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.CSI_Sequence attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.excn.EXCN_BadInput attribute) (pyrosetta.rosetta.utility.file.FileName attribute) (pyrosetta.rosetta.utility.file.PathName attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionCollection attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.OptionTypes attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.py.Value attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) __setitem__() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) __setstate__() (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __sizeof__() (pyrosetta.CD method) (pyrosetta.EnergyMethod method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerManager method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __str__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent attribute) (pyrosetta.rosetta.ObjexxFCL.Observer attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti attribute) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle attribute) (pyrosetta.rosetta.ObjexxFCL.Star attribute) (pyrosetta.rosetta.ObjexxFCL.byte attribute) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph attribute) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel attribute) (pyrosetta.rosetta.ObjexxFCL.ubyte attribute) (pyrosetta.rosetta.W128_T attribute) (pyrosetta.rosetta.basic.Emitter attribute) (pyrosetta.rosetta.basic.ExecutionResult attribute) (pyrosetta.rosetta.basic.JsonEmitter attribute) (pyrosetta.rosetta.basic.PyTracer attribute) (pyrosetta.rosetta.basic.Report attribute) (pyrosetta.rosetta.basic.Reporter attribute) (pyrosetta.rosetta.basic.Tracer attribute) (pyrosetta.rosetta.basic.TracerManager attribute) (pyrosetta.rosetta.basic.TracerOptions attribute) (pyrosetta.rosetta.basic.TracerPriority attribute) (pyrosetta.rosetta.basic.YamlEmitter attribute) (pyrosetta.rosetta.basic.datacache.BasicDataCache attribute) (pyrosetta.rosetta.basic.datacache.CacheableData attribute) (pyrosetta.rosetta.basic.datacache.CacheableString attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap attribute) (pyrosetta.rosetta.basic.datacache.CacheableStringMap attribute) (pyrosetta.rosetta.basic.datacache.ConstDataMap attribute) (pyrosetta.rosetta.basic.datacache.DataMap attribute) (pyrosetta.rosetta.basic.datacache.DiagnosticData attribute) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator attribute) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap attribute) (pyrosetta.rosetta.basic.mpi.listener_tags attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator attribute) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory attribute) (pyrosetta.rosetta.basic.resource_manager.ResourceStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator attribute) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream attribute) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream attribute) (pyrosetta.rosetta.core.chemical.AA attribute) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AddAtom attribute) (pyrosetta.rosetta.core.chemical.AddAtomAlias attribute) (pyrosetta.rosetta.core.chemical.AddBond attribute) (pyrosetta.rosetta.core.chemical.AddBondType attribute) (pyrosetta.rosetta.core.chemical.AddChi attribute) (pyrosetta.rosetta.core.chemical.AddChiRotamer attribute) (pyrosetta.rosetta.core.chemical.AddConnect attribute) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt attribute) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.AddProperty attribute) (pyrosetta.rosetta.core.chemical.Adduct attribute) (pyrosetta.rosetta.core.chemical.Ancestor attribute) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter attribute) (pyrosetta.rosetta.core.chemical.AtomICoor attribute) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager attribute) (pyrosetta.rosetta.core.chemical.AtomProperty attribute) (pyrosetta.rosetta.core.chemical.AtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.AutomorphismIterator attribute) (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) (pyrosetta.rosetta.core.chemical.BondConjugability attribute) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets attribute) (pyrosetta.rosetta.core.chemical.ChangeBondType attribute) (pyrosetta.rosetta.core.chemical.ChemicalManager attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms attribute) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming attribute) (pyrosetta.rosetta.core.chemical.ClearChiRotamers attribute) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton attribute) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteChildProton attribute) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom attribute) (pyrosetta.rosetta.core.chemical.DeleteProperty attribute) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi attribute) (pyrosetta.rosetta.core.chemical.DeleteVariantType attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.ElementSet attribute) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.GreekDistance attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter attribute) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID attribute) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type attribute) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet attribute) (pyrosetta.rosetta.core.chemical.MMAtomType attribute) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.Metapatch attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins attribute) (pyrosetta.rosetta.core.chemical.NCAARotLibPath attribute) (pyrosetta.rosetta.core.chemical.Patch attribute) (pyrosetta.rosetta.core.chemical.PatchCase attribute) (pyrosetta.rosetta.core.chemical.PatchOperation attribute) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter attribute) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.RamaPreproFilename attribute) (pyrosetta.rosetta.core.chemical.RamaPreproResname attribute) (pyrosetta.rosetta.core.chemical.RealFilter attribute) (pyrosetta.rosetta.core.chemical.RedefineChi attribute) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications attribute) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl attribute) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl attribute) (pyrosetta.rosetta.core.chemical.ResConnID attribute) (pyrosetta.rosetta.core.chemical.ResetBondLength attribute) (pyrosetta.rosetta.core.chemical.ResidueConnection attribute) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle attribute) (pyrosetta.rosetta.core.chemical.ResidueTypeSet attribute) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent attribute) (pyrosetta.rosetta.core.chemical.Selector_AA attribute) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG attribute) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME1 attribute) (pyrosetta.rosetta.core.chemical.Selector_NAME3 attribute) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS attribute) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY attribute) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION attribute) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE attribute) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive attribute) (pyrosetta.rosetta.core.chemical.SetAtomType attribute) (pyrosetta.rosetta.core.chemical.SetAtomicCharge attribute) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom attribute) (pyrosetta.rosetta.core.chemical.SetFormalCharge attribute) (pyrosetta.rosetta.core.chemical.SetICoor attribute) (pyrosetta.rosetta.core.chemical.SetIO_String attribute) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String attribute) (pyrosetta.rosetta.core.chemical.SetMMAtomType attribute) (pyrosetta.rosetta.core.chemical.SetNbrAtom attribute) (pyrosetta.rosetta.core.chemical.SetNbrRadius attribute) (pyrosetta.rosetta.core.chemical.SetOrientAtom attribute) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom attribute) (pyrosetta.rosetta.core.chemical.SetVirtualShadow attribute) (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.chemical.VirtualizeAll attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData attribute) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet attribute) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom attribute) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager attribute) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo attribute) (pyrosetta.rosetta.core.chemical.rna.RNA_Info attribute) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification attribute) (pyrosetta.rosetta.core.conformation.DefaultCubeHash attribute) (pyrosetta.rosetta.core.conformation.ResidueFactory attribute) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet attribute) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver attribute) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo attribute) (pyrosetta.rosetta.core.conformation.parametric.Parameters attribute) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet attribute) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.XYZEvent attribute) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.core.enzymes.EnzymeData attribute) (pyrosetta.rosetta.core.enzymes.EnzymeManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen attribute) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen attribute) (pyrosetta.rosetta.core.id.BondID attribute) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator attribute) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff attribute) (pyrosetta.rosetta.core.io.CisPeptideInformation attribute) (pyrosetta.rosetta.core.io.HELIXInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique attribute) (pyrosetta.rosetta.core.io.ModifiedResidueInformation attribute) (pyrosetta.rosetta.core.io.NomenclatureManager attribute) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo attribute) (pyrosetta.rosetta.core.io.ResidueInformation attribute) (pyrosetta.rosetta.core.io.SHEETInformation attribute) (pyrosetta.rosetta.core.io.SSBondInformation attribute) (pyrosetta.rosetta.core.io.pdb.RecordCollection attribute) (pyrosetta.rosetta.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder attribute) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.RawFileData attribute) (pyrosetta.rosetta.core.io.raw_data.RawStruct attribute) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText attribute) (pyrosetta.rosetta.core.io.rna.RNA_DataReader attribute) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast attribute) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator attribute) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentEnergy attribute) (pyrosetta.rosetta.core.io.silent.SilentFileData attribute) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator attribute) (pyrosetta.rosetta.core.io.silent.SilentStruct attribute) (pyrosetta.rosetta.core.io.silent.SilentStructCreator attribute) (pyrosetta.rosetta.core.kinematics.AtomTree attribute) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange attribute) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom attribute) (pyrosetta.rosetta.core.kinematics.tree.Atom_ attribute) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom attribute) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom attribute) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.BrentLineMinimization attribute) (pyrosetta.rosetta.core.optimization.CartesianMinimizer attribute) (pyrosetta.rosetta.core.optimization.CartesianMultifunc attribute) (pyrosetta.rosetta.core.optimization.ConvergenceTest attribute) (pyrosetta.rosetta.core.optimization.EItem attribute) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm attribute) (pyrosetta.rosetta.core.optimization.Minimizer attribute) (pyrosetta.rosetta.core.optimization.Multifunc attribute) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer attribute) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc attribute) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc attribute) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet attribute) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData attribute) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData attribute) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary attribute) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots attribute) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache attribute) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy attribute) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential attribute) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct attribute) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation attribute) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary attribute) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection attribute) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento attribute) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment attribute) (pyrosetta.rosetta.core.pack.task.ALLAA attribute) (pyrosetta.rosetta.core.pack.task.ALLAAwc attribute) (pyrosetta.rosetta.core.pack.task.ALLAAxc attribute) (pyrosetta.rosetta.core.pack.task.APOLA attribute) (pyrosetta.rosetta.core.pack.task.APOLAR attribute) (pyrosetta.rosetta.core.pack.task.AUTO attribute) (pyrosetta.rosetta.core.pack.task.EMPTY attribute) (pyrosetta.rosetta.core.pack.task.EX attribute) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF attribute) (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer attribute) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter attribute) (pyrosetta.rosetta.core.pack.task.NATAA attribute) (pyrosetta.rosetta.core.pack.task.NATRO attribute) (pyrosetta.rosetta.core.pack.task.NC attribute) (pyrosetta.rosetta.core.pack.task.NOTAA attribute) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS attribute) (pyrosetta.rosetta.core.pack.task.PIKAA attribute) (pyrosetta.rosetta.core.pack.task.PIKNA attribute) (pyrosetta.rosetta.core.pack.task.PIKRNA attribute) (pyrosetta.rosetta.core.pack.task.POLAR attribute) (pyrosetta.rosetta.core.pack.task.RESET attribute) (pyrosetta.rosetta.core.pack.task.ResfileCommand attribute) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ attribute) (pyrosetta.rosetta.core.pack.task.SCAN attribute) (pyrosetta.rosetta.core.pack.task.TARGET attribute) (pyrosetta.rosetta.core.pack.task.TaskFactory attribute) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer attribute) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet attribute) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative attribute) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers attribute) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric attribute) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation attribute) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection attribute) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides attribute) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset attribute) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG attribute) (pyrosetta.rosetta.core.pack.task.operation.OptH attribute) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents attribute) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator attribute) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking attribute) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign attribute) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion attribute) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator attribute) (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr attribute) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector attribute) (pyrosetta.rosetta.core.pose.datacache.ObserverCache attribute) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore attribute) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo attribute) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo attribute) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose attribute) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet attribute) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo attribute) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName attribute) (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.core.pose.signals.ConformationEvent attribute) (pyrosetta.rosetta.core.pose.signals.DestructionEvent attribute) (pyrosetta.rosetta.core.pose.signals.EnergyEvent attribute) (pyrosetta.rosetta.core.pose.signals.GeneralEvent attribute) (pyrosetta.rosetta.core.scoring.APBSConfig attribute) (pyrosetta.rosetta.core.scoring.APBSResult attribute) (pyrosetta.rosetta.core.scoring.APBSWrapper attribute) (pyrosetta.rosetta.core.scoring.AtomNeighbor attribute) (pyrosetta.rosetta.core.scoring.BB_Pos attribute) (pyrosetta.rosetta.core.scoring.CenListInfo attribute) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.DerivVectorPair attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.scoring.EnergyEdge attribute) (pyrosetta.rosetta.core.scoring.EnergyGraph attribute) (pyrosetta.rosetta.core.scoring.EnergyNode attribute) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSPotential attribute) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo attribute) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap attribute) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornPotential attribute) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo attribute) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.MembraneEmbed attribute) (pyrosetta.rosetta.core.scoring.MembranePotential attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed attribute) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential attribute) (pyrosetta.rosetta.core.scoring.MinimizationEdge attribute) (pyrosetta.rosetta.core.scoring.MinimizationGraph attribute) (pyrosetta.rosetta.core.scoring.MinimizationNode attribute) (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo attribute) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.NeighborList attribute) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.PDatom attribute) (pyrosetta.rosetta.core.scoring.PQR attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.Predicate attribute) (pyrosetta.rosetta.core.scoring.RDC_Rohl attribute) (pyrosetta.rosetta.core.scoring.ResRangePredicate attribute) (pyrosetta.rosetta.core.scoring.SS_Info attribute) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory attribute) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential attribute) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights attribute) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential attribute) (pyrosetta.rosetta.core.scoring.TMscoreStore attribute) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo attribute) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo attribute) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet attribute) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO attribute) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints attribute) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator attribute) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator attribute) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential attribute) (pyrosetta.rosetta.core.scoring.dna.BasePartner attribute) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential attribute) (pyrosetta.rosetta.core.scoring.dssp.Dssp attribute) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann attribute) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.etable.Etable attribute) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator attribute) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair attribute) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion attribute) (pyrosetta.rosetta.core.scoring.etable.MembEtable attribute) (pyrosetta.rosetta.core.scoring.etable.SplineParameters attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann attribute) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering attribute) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc attribute) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl attribute) (pyrosetta.rosetta.core.scoring.func.XYZ_Func attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType attribute) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy attribute) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo attribute) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase attribute) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy attribute) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty attribute) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator attribute) (pyrosetta.rosetta.core.scoring.membrane.MembraneData attribute) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod attribute) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator attribute) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType attribute) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase attribute) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator attribute) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy attribute) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator attribute) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMLJScore attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary attribute) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore attribute) (pyrosetta.rosetta.core.scoring.packing.HolesResult attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex attribute) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram attribute) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential attribute) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo attribute) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy attribute) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod attribute) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager attribute) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator attribute) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator attribute) (pyrosetta.rosetta.core.scoring.sc._RESULTS attribute) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ attribute) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector attribute) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector attribute) (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BinSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange attribute) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector attribute) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector attribute) (pyrosetta.rosetta.core.sequence.ABEGO attribute) (pyrosetta.rosetta.core.sequence.ABEGOManager attribute) (pyrosetta.rosetta.core.sequence.Line attribute) (pyrosetta.rosetta.core.sequence.SSManager attribute) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher attribute) (pyrosetta.rosetta.core.sequence.SequenceCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter attribute) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor attribute) (pyrosetta.rosetta.numeric.expression_parser.AndExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode attribute) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue attribute) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator attribute) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression attribute) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression attribute) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state attribute) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner attribute) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree attribute) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher attribute) (pyrosetta.rosetta.numeric.kdtree.KDPointList attribute) (pyrosetta.rosetta.numeric.model_quality.RmsData attribute) (pyrosetta.rosetta.numeric.random.RandomGenerator attribute) (pyrosetta.rosetta.numeric.random.standard_RG attribute) (pyrosetta.rosetta.numeric.random.uniform_RG attribute) (pyrosetta.rosetta.protocols.LoopRebuild attribute) (pyrosetta.rosetta.protocols.LoopRefine attribute) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover attribute) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication attribute) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover attribute) (pyrosetta.rosetta.protocols.analysis.InterfaceData attribute) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData attribute) (pyrosetta.rosetta.protocols.anchored_design.Anchor attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData attribute) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator attribute) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser attribute) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions attribute) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser attribute) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop attribute) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer attribute) (pyrosetta.rosetta.protocols.antibody.H3CterInsert attribute) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 attribute) (pyrosetta.rosetta.protocols.antibody.PDBLandmark attribute) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet attribute) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData attribute) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol attribute) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator attribute) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions attribute) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler attribute) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster attribute) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq attribute) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain attribute) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence attribute) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager attribute) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector attribute) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation attribute) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors attribute) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler attribute) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover attribute) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker attribute) (pyrosetta.rosetta.protocols.backrub.BackrubMover attribute) (pyrosetta.rosetta.protocols.backrub.BackrubSegment attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 attribute) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering attribute) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover attribute) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver attribute) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator attribute) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover attribute) (pyrosetta.rosetta.protocols.checkpoint.Timer attribute) (pyrosetta.rosetta.protocols.cluster.APCluster attribute) (pyrosetta.rosetta.protocols.cluster.DataPoint attribute) (pyrosetta.rosetta.protocols.cluster.Exemplar attribute) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter attribute) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter attribute) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager attribute) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap attribute) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo attribute) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints attribute) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator attribute) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator attribute) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator attribute) (pyrosetta.rosetta.protocols.contact_map.Contact attribute) (pyrosetta.rosetta.protocols.contact_map.ContactPartner attribute) (pyrosetta.rosetta.protocols.cryst.CheshireCell attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication attribute) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror attribute) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.Picker attribute) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber attribute) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover attribute) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector attribute) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector attribute) (pyrosetta.rosetta.protocols.dna.PositionType attribute) (pyrosetta.rosetta.protocols.docking.DockingEnsemble attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter attribute) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy attribute) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation attribute) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter attribute) (pyrosetta.rosetta.protocols.docking.SlideIntoContact attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator attribute) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover attribute) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo attribute) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover attribute) (pyrosetta.rosetta.protocols.electron_density.ReportFSC attribute) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc attribute) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover attribute) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement attribute) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts attribute) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf attribute) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison attribute) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface attribute) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter attribute) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter attribute) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs attribute) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy attribute) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination attribute) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter attribute) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover attribute) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter attribute) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior attribute) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover attribute) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator attribute) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory attribute) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder attribute) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter attribute) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation attribute) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter attribute) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter attribute) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator attribute) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory attribute) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBDefType attribute) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeatures attribute) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator attribute) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator attribute) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator attribute) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover attribute) (pyrosetta.rosetta.protocols.filters.CombinedFilter attribute) (pyrosetta.rosetta.protocols.filters.CompoundFilter attribute) (pyrosetta.rosetta.protocols.filters.FilterCollection attribute) (pyrosetta.rosetta.protocols.filters.FilterCreator attribute) (pyrosetta.rosetta.protocols.filters.IfThenFilter attribute) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels attribute) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager attribute) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer attribute) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat attribute) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge attribute) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign attribute) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma attribute) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator attribute) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator attribute) (pyrosetta.rosetta.protocols.forge.build.Bridge attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction attribute) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.BuildManager attribute) (pyrosetta.rosetta.protocols.forge.build.ConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowLeft attribute) (pyrosetta.rosetta.protocols.forge.build.GrowRight attribute) (pyrosetta.rosetta.protocols.forge.build.Interval attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight attribute) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap attribute) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild attribute) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG attribute) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG attribute) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator attribute) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo attribute) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG attribute) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent attribute) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore attribute) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker attribute) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule attribute) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunk attribute) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter attribute) (pyrosetta.rosetta.protocols.frag_picker.VallProvider attribute) (pyrosetta.rosetta.protocols.frag_picker.VallResidue attribute) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector attribute) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity attribute) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity attribute) (pyrosetta.rosetta.protocols.frags.VallData attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer attribute) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer attribute) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover attribute) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover attribute) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover attribute) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork attribute) (pyrosetta.rosetta.protocols.hbnet.HBondEdge attribute) (pyrosetta.rosetta.protocols.hbnet.HBondNode attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct attribute) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct attribute) (pyrosetta.rosetta.protocols.hbnet.polar_atom attribute) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper attribute) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) (pyrosetta.rosetta.protocols.helical_bundle.DoFType attribute) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc attribute) (pyrosetta.rosetta.protocols.helical_bundle.PertType attribute) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters attribute) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet attribute) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged attribute) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory attribute) (pyrosetta.rosetta.protocols.idealize.IdealizeMover attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputter attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator attribute) (pyrosetta.rosetta.protocols.jd2.JobsContainer attribute) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter attribute) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer attribute) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase attribute) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager attribute) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor attribute) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive attribute) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter attribute) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter attribute) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.BasicJob attribute) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor attribute) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor attribute) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.Interval attribute) (pyrosetta.rosetta.protocols.jumping.JumpSelector attribute) (pyrosetta.rosetta.protocols.jumping.JumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings attribute) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup attribute) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle attribute) (pyrosetta.rosetta.protocols.jumping.SheetBuilder attribute) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary attribute) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary attribute) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem attribute) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution attribute) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters attribute) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker attribute) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions attribute) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker attribute) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap attribute) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol attribute) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader attribute) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints attribute) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow attribute) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator attribute) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler attribute) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber attribute) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover attribute) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol attribute) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner attribute) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid attribute) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom attribute) (pyrosetta.rosetta.protocols.loophash.FastGapMover attribute) (pyrosetta.rosetta.protocols.loophash.LeapIndex attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator attribute) (pyrosetta.rosetta.protocols.loophash.LoopHashMap attribute) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile attribute) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory attribute) (pyrosetta.rosetta.protocols.loops.Loop_lt attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator attribute) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator attribute) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader attribute) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator attribute) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop attribute) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator attribute) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData attribute) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM attribute) (pyrosetta.rosetta.protocols.match.BfactorMPM attribute) (pyrosetta.rosetta.protocols.match.HitHasher attribute) (pyrosetta.rosetta.protocols.match.HitNeighborFinder attribute) (pyrosetta.rosetta.protocols.match.MatchCounter attribute) (pyrosetta.rosetta.protocols.match.MatchPositionModifier attribute) (pyrosetta.rosetta.protocols.match.Matcher attribute) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM attribute) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash attribute) (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM attribute) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM attribute) (pyrosetta.rosetta.protocols.match.TaskOperationMPM attribute) (pyrosetta.rosetta.protocols.match.VoxelSetIterator attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm attribute) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory attribute) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue attribute) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare attribute) (pyrosetta.rosetta.protocols.match.match_dspos1 attribute) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter attribute) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator attribute) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper attribute) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter attribute) (pyrosetta.rosetta.protocols.match.upstream.BuildSet attribute) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler attribute) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData attribute) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry attribute) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMover attribute) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler attribute) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.mean_field.ResHasher attribute) (pyrosetta.rosetta.protocols.mean_field.ResPred attribute) (pyrosetta.rosetta.protocols.medal.MedalMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.FlipMover attribute) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility attribute) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover attribute) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMover attribute) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover attribute) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TiltMover attribute) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover attribute) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix attribute) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles attribute) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef attribute) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover attribute) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator attribute) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints attribute) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data attribute) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes attribute) (pyrosetta.rosetta.protocols.moves.CyclicMover attribute) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo attribute) (pyrosetta.rosetta.protocols.moves.FilterReporterMover attribute) (pyrosetta.rosetta.protocols.moves.GeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc attribute) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover attribute) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil attribute) (pyrosetta.rosetta.protocols.moves.MoverCreator attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) (pyrosetta.rosetta.protocols.moves.ResId attribute) (pyrosetta.rosetta.protocols.moves.StatsType attribute) (pyrosetta.rosetta.protocols.moves.VectorPoseMover attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax attribute) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss attribute) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker attribute) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc attribute) (pyrosetta.rosetta.protocols.neighbor.Neighborhood attribute) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance attribute) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover attribute) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule attribute) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap attribute) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.Resonance attribute) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList attribute) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover attribute) (pyrosetta.rosetta.protocols.nonlocal.Chunk attribute) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate attribute) (pyrosetta.rosetta.protocols.nonlocal.Policy attribute) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate attribute) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy attribute) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer attribute) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc attribute) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData attribute) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc attribute) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator attribute) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker attribute) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy attribute) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy attribute) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoader attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator attribute) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory attribute) (pyrosetta.rosetta.protocols.parser.FragSetLoader attribute) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader attribute) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader attribute) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader attribute) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader attribute) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter attribute) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver attribute) (pyrosetta.rosetta.protocols.pockets.CCluster attribute) (pyrosetta.rosetta.protocols.pockets.CClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid attribute) (pyrosetta.rosetta.protocols.pockets.EggshellGrid attribute) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PCluster attribute) (pyrosetta.rosetta.protocols.pockets.PClusterSet attribute) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator attribute) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc attribute) (pyrosetta.rosetta.protocols.pockets.PocketGrid attribute) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid attribute) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt attribute) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter attribute) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter attribute) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.Filter attribute) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector attribute) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue attribute) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences attribute) (pyrosetta.rosetta.protocols.protein_interface_design.Revert attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover attribute) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet attribute) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover attribute) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover attribute) (pyrosetta.rosetta.protocols.relax.CentroidRelax attribute) (pyrosetta.rosetta.protocols.relax.ClassicRelax attribute) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator attribute) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover attribute) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector attribute) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector attribute) (pyrosetta.rosetta.protocols.rigid.Direction attribute) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover attribute) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.Partner attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover attribute) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover attribute) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover attribute) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover attribute) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover attribute) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager attribute) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover attribute) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer attribute) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo attribute) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler attribute) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser attribute) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman attribute) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory attribute) (pyrosetta.rosetta.protocols.scoring.InterchainPotential attribute) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover attribute) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory attribute) (pyrosetta.rosetta.protocols.sewing.Basis attribute) (pyrosetta.rosetta.protocols.sewing.Hasher attribute) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile attribute) (pyrosetta.rosetta.protocols.sewing.SegmentGraph attribute) (pyrosetta.rosetta.protocols.sewing.SewGraph attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator attribute) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory attribute) (pyrosetta.rosetta.protocols.sic_dock.JointScore attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak attribute) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids attribute) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.Operator attribute) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseComment attribute) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData attribute) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator attribute) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance attribute) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid attribute) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter attribute) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData attribute) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover attribute) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb attribute) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover attribute) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover attribute) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer attribute) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator attribute) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology attribute) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA attribute) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover attribute) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator attribute) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion attribute) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover attribute) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot attribute) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover attribute) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData attribute) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover attribute) (pyrosetta.rosetta.protocols.simple_moves.TrialResult attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins attribute) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover attribute) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact attribute) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover attribute) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup attribute) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover attribute) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover attribute) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser attribute) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator attribute) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover attribute) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator attribute) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap attribute) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup attribute) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter attribute) (pyrosetta.rosetta.protocols.toolbox.KCluster attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterData attribute) (pyrosetta.rosetta.protocols.toolbox.KClusterElement attribute) (pyrosetta.rosetta.protocols.toolbox.KMedoid attribute) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork attribute) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList attribute) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO attribute) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover attribute) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation attribute) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator attribute) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer attribute) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitBase attribute) (pyrosetta.rosetta.protocols.wum.WorkUnitList attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper attribute) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore attribute) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs attribute) (pyrosetta.rosetta.utility.SimulateMPI attribute) (pyrosetta.rosetta.utility.graph.Digraph attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeList attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement attribute) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeList attribute) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator attribute) (pyrosetta.rosetta.utility.graph.EdgeListElement attribute) (pyrosetta.rosetta.utility.graph.EdgeListIterator attribute) (pyrosetta.rosetta.utility.graph.Graph attribute) (pyrosetta.rosetta.utility.io.FileContentsMap attribute) (pyrosetta.rosetta.utility.io.icstream attribute) (pyrosetta.rosetta.utility.io.irstream attribute) (pyrosetta.rosetta.utility.io.izstream attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) (pyrosetta.rosetta.utility.io.ocstream attribute) (pyrosetta.rosetta.utility.io.orstream attribute) (pyrosetta.rosetta.utility.io.ozstream attribute) (pyrosetta.rosetta.utility.keys.Key attribute) (pyrosetta.rosetta.utility.keys.NoClient attribute) (pyrosetta.rosetta.utility.options.AnyOptionKey attribute) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanOption attribute) (pyrosetta.rosetta.utility.options.BooleanOptionKey attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOption attribute) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.FileOption attribute) (pyrosetta.rosetta.utility.options.FileOptionKey attribute) (pyrosetta.rosetta.utility.options.FileVectorOption attribute) (pyrosetta.rosetta.utility.options.FileVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerOption attribute) (pyrosetta.rosetta.utility.options.IntegerOptionKey attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOption attribute) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.Option attribute) (pyrosetta.rosetta.utility.options.OptionKey attribute) (pyrosetta.rosetta.utility.options.OptionTypes attribute) (pyrosetta.rosetta.utility.options.PathOption attribute) (pyrosetta.rosetta.utility.options.PathOptionKey attribute) (pyrosetta.rosetta.utility.options.PathVectorOption attribute) (pyrosetta.rosetta.utility.options.PathVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.RealOption attribute) (pyrosetta.rosetta.utility.options.RealOptionKey attribute) (pyrosetta.rosetta.utility.options.RealVectorOption attribute) (pyrosetta.rosetta.utility.options.RealVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption attribute) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.ScalarOption attribute) (pyrosetta.rosetta.utility.options.ScalarOptionKey attribute) (pyrosetta.rosetta.utility.options.StringOption attribute) (pyrosetta.rosetta.utility.options.StringOptionKey attribute) (pyrosetta.rosetta.utility.options.StringVectorOption attribute) (pyrosetta.rosetta.utility.options.StringVectorOptionKey attribute) (pyrosetta.rosetta.utility.options.VectorOption attribute) (pyrosetta.rosetta.utility.options.VectorOptionKey attribute) (pyrosetta.rosetta.utility.py.Base attribute) (pyrosetta.rosetta.utility.py.PyExitCallback attribute) (pyrosetta.rosetta.utility.recent_history_queue attribute) (pyrosetta.rosetta.utility.signals.Link attribute) (pyrosetta.rosetta.utility.signals.LinkUnit attribute) (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) (pyrosetta.rosetta.utility.subset_mapping attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) __str__() (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.py.Value method) __sub__() (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) __subclasshook__() (pyrosetta.CD method) (pyrosetta.EnergyMethod method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerManager method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceConfiguration method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoorAtomID.Type method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.SplineParameters method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.__ATTEN_ENUM__ method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.hbnet.hbond_net_struct method) (pyrosetta.rosetta.protocols.hbnet.hbond_res_struct method) (pyrosetta.rosetta.protocols.hbnet.polar_atom method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.DoFType method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.PertType method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.sewing.Basis method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TrialResult method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) __weakref__ (pyrosetta.CD attribute) (pyrosetta.EnergyMethod attribute) _add_weights_from_file() (pyrosetta.rosetta.core.scoring.ScoreFunction method) _add_weights_from_stream() (pyrosetta.rosetta.core.scoring.ScoreFunction method) _M_write() (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Tracer method) _notebook_logging_callback() (in module pyrosetta.logging_support) _pmatch() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) _read_file() (pyrosetta.rosetta.core.io.silent.SilentFileData method) _RESULTS (class in pyrosetta.rosetta.core.scoring.sc) _rosetta_database_from_env() (in module pyrosetta) _static_type_name() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) _write_silent_struct() (pyrosetta.rosetta.core.io.silent.SilentFileData method)