Index – T

T() (in module pyrosetta.rosetta.basic) t_str() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) tab_prefixed() (pyrosetta.rosetta.utility.options.OptionCollection method) table_exists() (in module pyrosetta.rosetta.basic.database) TabooSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) tabulate() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) tag() (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairType method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) tag_from_line() (in module pyrosetta.rosetta.core.chemical) tag_from_pdb_fname() (in module pyrosetta.rosetta.core.scoring.motif) tag_from_pose() (in module pyrosetta.rosetta.core.pose) tag_into_pose() (in module pyrosetta.rosetta.core.pose) tag_time() (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) tags() (pyrosetta.rosetta.core.io.silent.SilentFileData method) tail() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) TailFunction (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) take_coordinates_from_pose() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) takeoff_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) takeoff_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) TalosSSSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) targ_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) targ_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) TARGET (class in pyrosetta.rosetta.core.pack.task) target() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) target_chain() (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) target_pose_start() (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) target_res() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) target_res_for_geom_cst() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) target_residues() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) target_seq() (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) target_sequence() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) target_type() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) TargetPocketGrid (class in pyrosetta.rosetta.protocols.pockets) targetPocketHeuristicScore() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketHydrophobicProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketPolarProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketSolventSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketVolume() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) task() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover 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.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) task_factory() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.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.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover 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.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) task_initialized() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) task_is_valid() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) task_op_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) task_op_schema_empty() (in module pyrosetta.rosetta.core.pack.task.operation) task_op_schema_w_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) task_scaling() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) task_string() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) TaskAwareCsts (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) TaskAwareMinMover (class in pyrosetta.rosetta.protocols.simple_moves) TaskFactory (class in pyrosetta.rosetta.core.pack.task) TaskOperationCreator (class in pyrosetta.rosetta.core.pack.task.operation) TaskOperationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) TaskOperationLoader (class in pyrosetta.rosetta.protocols.parser) TaskOperationMPM (class in pyrosetta.rosetta.protocols.match) TaskSelector (class in pyrosetta.rosetta.protocols.residue_selectors) TBMB_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) temp() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) temp1() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) temp2() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) temp3() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) temp4() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) temp_file() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) temperature() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover 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.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover 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.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) temperature_level() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) temperature_move() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) TemperatureController (class in pyrosetta.rosetta.protocols.canonical_sampling) temperatures() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) TemperedDocking (class in pyrosetta.rosetta.protocols.docking) tempering() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) TemperingBase (class in pyrosetta.rosetta.protocols.canonical_sampling) template_file() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) template_name() (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) template_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) TemplateFragmentClaimer (class in pyrosetta.rosetta.protocols.topology_broker) TemplateHistory (class in pyrosetta.rosetta.protocols.hybridization) TemplateJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) templates_from_cmd_line() (in module pyrosetta.rosetta.protocols.comparative_modeling) temporarily_fix_everything() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) temporarily_set_pack_residue() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) temps() (pyrosetta.rosetta.core.io.ResidueInformation method) tenA_neighbor_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) tensor() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) terCount() (pyrosetta.rosetta.core.io.ResidueInformation method) termini_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) TerminiConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) test_all_mg_hydration_frames() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) test_chunk() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) test_if_schema_is_valid() (in module pyrosetta.rosetta.utility.tag) test_move() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) test_res_res_aln() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) testNeighbor() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) tether_jump() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) TheozymeInvrotTree (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) thermal_sampler_output_min_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) thermal_sampler_temperature() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) ThermalMinimizer (class in pyrosetta.rosetta.protocols.recces.scratch) ThermalSamplingMover (class in pyrosetta.rosetta.protocols.recces.scratch) ThermodynamicData (class in pyrosetta.rosetta.protocols.simple_moves) ThermodynamicMover (class in pyrosetta.rosetta.protocols.canonical_sampling) ThermodynamicObserver (class in pyrosetta.rosetta.protocols.canonical_sampling) theta() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.pose.Pose method) thickness() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) thread_sequence_on_pose() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) ThreadingJob (class in pyrosetta.rosetta.protocols.comparative_modeling) ThreadingJobInputter (class in pyrosetta.rosetta.protocols.comparative_modeling) ThreadSequenceOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) threshold() (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter 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.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) tighten_memory() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.pose.PDBInfo method) tilt1_center() (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) tilt1_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) tilt2_center() (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) tilt2_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) TiltMover (class in pyrosetta.rosetta.protocols.membrane) TiltMoverCreator (class in pyrosetta.rosetta.protocols.membrane) time_to_checkpoint() (pyrosetta.rosetta.protocols.checkpoint.Timer method) Timer (class in pyrosetta.rosetta.protocols.checkpoint) timestamp() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.jd2.Job method) timestamp_short() (in module pyrosetta.rosetta.utility) title() (pyrosetta.rosetta.core.io.HeaderInformation method) tm_projection_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) TMA_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) tmpbuf() (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) TMscoreStore (class in pyrosetta.rosetta.core.scoring) to_all_atom() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) to_bare_name() (pyrosetta.rosetta.utility.file.FileName method) to_centroid() (in module pyrosetta.rosetta.protocols.medal) (in module pyrosetta.rosetta.protocols.star) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) to_default() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) to_degrees() (in module pyrosetta.rosetta.numeric.conversions) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) to_do() (pyrosetta.rosetta.protocols.jd2.Job method) to_left() (in module pyrosetta.rosetta.core.membrane) to_local_name() (pyrosetta.rosetta.utility.file.FileName method) to_multichain_pose() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) to_pose() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) to_radians() (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) to_string() (in module pyrosetta.rosetta.core.id) (in module pyrosetta.rosetta.core.pose.full_model_info) (in module pyrosetta.rosetta.core.scoring.rna) (in module pyrosetta.rosetta.numeric.interpolation) (in module pyrosetta.rosetta.protocols.moves) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) toFloat() (in module pyrosetta.rosetta.protocols.cluster.calibur) toInt() (in module pyrosetta.rosetta.protocols.cluster.calibur) token_type_name() (in module pyrosetta.rosetta.numeric.expression_parser) tokenize() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) tokenize_line() (in module pyrosetta.rosetta.core.pack.task) tolerance() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover 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.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) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) tolerated_overlap() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) ToolboxKeys (class in pyrosetta.rosetta.protocols.loop_modeling) top_fragments() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) TopNByProperty (class in pyrosetta.rosetta.protocols.pose_selectors) topological_match_to() (pyrosetta.rosetta.core.kinematics.AtomTree method) topological_observers() (pyrosetta.rosetta.core.kinematics.AtomTree method)

topological_sort() (in module pyrosetta.rosetta.utility.graph) topology_broker() (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) TopologyBrokerMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) TopologyClaimerFactory (class in pyrosetta.rosetta.protocols.topology_broker) tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) torsion() (in module pyrosetta.rosetta.numeric.kinematic_closure) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.pose.Pose method) torsion2big_bin() (in module pyrosetta.rosetta.protocols.frags) torsion2big_bin_id() (in module pyrosetta.rosetta.protocols.frag_picker.quota) torsion2index() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion2index_level1() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion2index_level2() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion2index_level3() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion2index_level4() (pyrosetta.rosetta.core.sequence.ABEGOManager method) torsion_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) torsion_angle_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) torsion_constraints_from_chi_rotamers() (in module pyrosetta.rosetta.protocols.ligand_docking) torsion_constraints_from_rotamers() (in module pyrosetta.rosetta.protocols.ligand_docking) torsion_ct_name() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) torsion_delta() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) torsion_features_string() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) torsion_id() (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) torsion_id_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) torsion_id_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) torsion_id_ranges() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover 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.UniformSphereTransMover 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.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover 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.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) Torsion_Info (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) torsion_name() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) torsion_sample_value() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) torsion_scale_factor() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) torsion_type_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) torsion_type_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) torsional_derivative_from_cartesian_derivatives() (in module pyrosetta.rosetta.core.optimization) TorsionBinSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) TorsionDOFMover (class in pyrosetta.rosetta.protocols.simple_moves) TorsionFragment (class in pyrosetta.rosetta.protocols.frags) TorsionFragmentLibrary (class in pyrosetta.rosetta.protocols.frags) TorsionID (class in pyrosetta.rosetta.core.id) TorsionID_Range (class in pyrosetta.rosetta.core.id) TorsionRestrictedKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) torsions() (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) TorsionSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) TorsionSweepingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) TorsionType (class in pyrosetta.rosetta.core.id) total_accepts() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) total_atoms() (pyrosetta.rosetta.core.pose.Pose method) total_counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) total_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) total_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) total_energy_from_pose() (in module pyrosetta.rosetta.core.pose) total_nr_jobs() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) total_number_abego() (pyrosetta.rosetta.core.sequence.ABEGOManager method) total_proposed() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) total_residue() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) total_score() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) total_score_of_last_considered_pose() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) total_size() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) total_standard_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) total_trials() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) Tracer (class in pyrosetta.rosetta.basic) tracer_options() (pyrosetta.rosetta.basic.Tracer method) TracerManager (class in pyrosetta.rosetta.basic) TracerOptions (class in pyrosetta.rosetta.basic) TracerPriority (class in pyrosetta.rosetta.basic) track_insertion_order() (pyrosetta.rosetta.basic.resource_manager.JobOptions method) traits() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) traits_string() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) TrajectoryMapFeaturesCreator (class in pyrosetta.rosetta.protocols.features) TrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) trans_axis() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) trans_magnitude() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) trans_omega() (in module pyrosetta.rosetta.protocols.forge.methods) trans_pose() (in module pyrosetta.rosetta.protocols.sic_dock) transaction_mode_from_name() (in module pyrosetta.rosetta.utility.sql_database) transfer_constraint_set() (pyrosetta.rosetta.core.pose.Pose method) transfer_jumps() (in module pyrosetta.rosetta.core.pose) transfer_phi_psi() (in module pyrosetta.rosetta.core.pose) transform() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) transform_Ax_plus_b_recursive() (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) transform_model() (pyrosetta.rosetta.protocols.sewing.Hasher method) transform_moving_partition_to_origin() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) transform_percentile() (in module pyrosetta.rosetta.numeric.kdtree) transform_percentile_single_pt() (in module pyrosetta.rosetta.numeric.kdtree) transform_res_to_subunit() (in module pyrosetta.rosetta.protocols.loop_grower) transform_to_closest_symmunit() (in module pyrosetta.rosetta.protocols.loop_grower) TransformIntoMembraneMover (class in pyrosetta.rosetta.protocols.membrane) TransformIntoMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane) transforms_uptodate() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) transitive_map() (in module pyrosetta.rosetta.core.sequence) translate() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) translate_and_rotate_residue_to_origin() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) translate_by() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) translate_pose() (in module pyrosetta.toolbox.numpy_utils) translate_virtual_anchor_to_first_rigid_body() (in module pyrosetta.rosetta.protocols.rna.denovo) translation() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) translation_along_axis() (pyrosetta.rosetta.core.kinematics.Jump method) TranslationFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) TranslationMover (class in pyrosetta.rosetta.protocols.membrane) TranslationMoverCreator (class in pyrosetta.rosetta.protocols.membrane) TranslationRotationMover (class in pyrosetta.rosetta.protocols.membrane) TranslationRotationMoverCreator (class in pyrosetta.rosetta.protocols.membrane) transpose_product() (in module pyrosetta.rosetta.numeric) transpose_so3() (in module pyrosetta.rosetta.numeric.fourier) tree_from_jumps_and_cuts() (pyrosetta.rosetta.core.kinematics.FoldTree method) tree_init() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) trial_counter() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) TrialCounterObserver (class in pyrosetta.rosetta.protocols.canonical_sampling) TrialCounterObserverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) TrialMover (class in pyrosetta.rosetta.protocols.moves) TrialResult (class in pyrosetta.rosetta.protocols.simple_moves) tries() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) trigger_accept() (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) trim() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.utility.options.OptionCollection method) trim_back_sequence_mapping() (in module pyrosetta.rosetta.protocols.loops) trim_framework() (in module pyrosetta.rosetta.protocols.antibody.grafting) trim_neighbors_by_distance() (in module pyrosetta.rosetta.core.select) trim_scores() (pyrosetta.rosetta.protocols.sewing.Hasher method) trim_to_single_repeat() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) trim_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) trimmed() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.utility.options.OptionCollection method) trimmed_compare() (in module pyrosetta.rosetta.utility) trimmed_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) trimmed_whitespace_range() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) truefalseoption() (in module pyrosetta.rosetta.basic.options) truncate_abego() (in module pyrosetta.rosetta.protocols.denovo_design.components) trust_fold_tree() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) trytry_ifstream_open() (in module pyrosetta.rosetta.utility.file) trytry_ofstream_open() (in module pyrosetta.rosetta.utility.file) turn_off_cter_insert() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) turn_off_H3_filter() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) turn_off_rna_chem_map_during_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) twelveA_neighbor_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) twist_level() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) two_parts_chain1() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) two_step() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) type() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Residue 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.SingleResidueFragData method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl 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.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.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.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.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.NullPoseFolder 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.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.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) type_for_fake_atoms() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) type_name() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator 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.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator 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.jumping.BaseJumpSetup 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.SheetBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) type_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) type_ptr() (pyrosetta.rosetta.core.conformation.Residue method) type_set_mode_from_string() (in module pyrosetta.rosetta.core.chemical) type_set_tag() (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) type_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) types() (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.Patch method) types_to_avoid() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) TypeSetMode (class in pyrosetta.rosetta.core.chemical)