Index – T

T (class in pyrosetta.rosetta.protocols.features.RelevantResiduesMode) t (pyrosetta.rosetta.numeric.Py_xyzTransform_double property) (pyrosetta.rosetta.numeric.xyzTransform_double_t property) (pyrosetta.rosetta.numeric.xyzTransform_float_t property) t_debug (pyrosetta.rosetta.basic.TracerPriority attribute) t_error (pyrosetta.rosetta.basic.TracerPriority attribute) t_fatal (pyrosetta.rosetta.basic.TracerPriority attribute) t_info (pyrosetta.rosetta.basic.TracerPriority attribute) t_jump() (pyrosetta.rosetta.protocols.moves.SimulatedTempering method) T_LOOP (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) t_str() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) t_trace (pyrosetta.rosetta.basic.TracerPriority attribute) t_warning (pyrosetta.rosetta.basic.TracerPriority attribute) Ta (pyrosetta.rosetta.core.chemical.element.Elements attribute) TAB_DIR (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) tab_prefixed() (pyrosetta.rosetta.utility.options.OptionCollection static method) table_exists() (in module pyrosetta.rosetta.basic.database) tableID (class in pyrosetta.rosetta.core.scoring) TableLookupEtableEnergy (class in pyrosetta.rosetta.core.scoring.etable) TableLookupEvaluator (class in pyrosetta.rosetta.core.scoring.etable) TabooSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) tabulate() (pyrosetta.rosetta.core.scoring.saxs.FormFactor method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) Tag (class in pyrosetta.rosetta.utility.tag) tag (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent property) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent property) (pyrosetta.rosetta.core.conformation.signals.LengthEvent property) (pyrosetta.rosetta.core.optimization.EItem property) (pyrosetta.rosetta.protocols.qsar.qsarOptData property) tag() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) (pyrosetta.rosetta.core.import_pose.libraries.BasePairType method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.numeric.RocPoint method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) tag_ (pyrosetta.rosetta.core.fragment.CacheWrapper_protocols_simple_moves_GunnTuple_core_fragment_MapCacheUnit_protocols_simple_moves_GunnTuple_t property) (pyrosetta.rosetta.core.fragment.FragCache_protocols_simple_moves_GunnTuple_t property) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator property) tag_along_chain_ids() (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) tag_along_jumps() (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) tag_along_residues (pyrosetta.rosetta.protocols.ligand_docking.Ligand_info property) tag_along_residues() (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) TAG_DEFINITION (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) tag_disulfide() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) tag_disulfides() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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_list_for_input_pose_id() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager method) tag_manager() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) tag_map_ (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug property) tag_time() (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) TagDefinition (class in pyrosetta.rosetta.protocols.stepwise.screener) TagManager (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) TagPoseWithRefinementStatsMover (class in pyrosetta.rosetta.protocols.cryst) TagPoseWithRefinementStatsMoverCreator (class in pyrosetta.rosetta.protocols.cryst) tags (pyrosetta.io.silent_file_map.SilentFileMap property) tags() (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) tags_ (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug property) tail() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) tail_fold_tree() (pyrosetta.rosetta.protocols.splice.Splice method) tail_mover() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) tail_seg() (pyrosetta.rosetta.protocols.splice.SpliceManager method) tail_segment() (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) TailFunction (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) (class in pyrosetta.rosetta.core.scoring.netcharge_energy) TailSegmentMover (class in pyrosetta.rosetta.protocols.splice) TailSegmentMoverCreator (class in pyrosetta.rosetta.protocols.splice) TailsScoreMover (class in pyrosetta.rosetta.protocols.simple_moves) take_Base_pointer() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_Base_reference() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_Base_SP() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_coordinates_from_pose() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) take_O_1A_pointer() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_O_1A_reference() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_O_1A_SP() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_O_2A_pointer() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_O_2A_reference() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_O_2A_SP() (in module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) take_out_cutpoints() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.TransientCutpointHandler method) take_pose_op() (in module pyrosetta.rosetta.protocols.toolbox) 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) TANDEM_GA_SHEARED (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) TANDEM_GA_WATSON_CRICK (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) targ_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) targ_atom_names() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) targ_base2_atom_names() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) targ_base_atom_names() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) targ_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) targ_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions 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_clash (pyrosetta.rosetta.core.scoring.ScoreType attribute) target_clash_pdb() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) target_conformer() (pyrosetta.rosetta.protocols.motifs.MotifHit method) target_conformers_map() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) target_constel() (in module pyrosetta.rosetta.protocols.constel) target_downstream_res() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) target_net_charge() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) target_net_charge_active() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) target_pose_start() (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) target_positions() (pyrosetta.rosetta.protocols.motifs.BuildPosition method) (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) target_region() (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) target_region_string() (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) target_res() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) target_res_for_geom_cst() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) target_residues() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) target_seq() (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) target_sequence() (pyrosetta.rosetta.protocols.abinitio.Templates method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) target_stub (pyrosetta.rosetta.protocols.hotspot_hashing.ConstPattern property) target_total_residue() (pyrosetta.rosetta.protocols.abinitio.Templates method) target_type() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) TargetClashEnergy (class in pyrosetta.rosetta.protocols.scoring.methods) TargetClashEnergyCreator (class in pyrosetta.rosetta.protocols.scoring.methods) targeted_dna() (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) TargetPocketGrid (class in pyrosetta.rosetta.protocols.pockets) targetPocketHeuristicScore() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketHydrophobicProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketPolarProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketProteinSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketSolventSurface() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) targetPocketVolume() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) TargetRotamerCoords (class in pyrosetta.rosetta.protocols.match.downstream) task (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ReweightData property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) task() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.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.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.testing.BenchmarkBuildRotamersMover method) task_clear() (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) task_factory() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.optimize_weights.IterativeOptEDriver method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA 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.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) task_factory_set() (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) task_from_bool_mask() (in module pyrosetta.rosetta.core.pack.task.residue_selector) task_from_resnums() (in module pyrosetta.rosetta.core.pack.task.residue_selector) 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.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) task_name() (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) task_op_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.TaskOperationLoader static 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_operation_xml_schema_group_name() (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory static method) task_scaling() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.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) TaskAwareCstsCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) TaskAwareMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) TaskAwareMinMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) TaskAwareSASAFilter (class in pyrosetta.rosetta.protocols.simple_filters) TaskAwareSASAFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) TaskAwareScoreTypeFilter (class in pyrosetta.rosetta.protocols.simple_filters) TaskAwareScoreTypeFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) TaskAwareSymMinMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) TaskAwareSymMinMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) taskFactOP_ (pyrosetta.rosetta.protocols.hybridization.detailedControlsTagSetting property) TaskFactory (class in pyrosetta.rosetta.core.pack.task) TaskOperation (class in pyrosetta.rosetta.core.pack.task.operation) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) TaskOperationCreator (class in pyrosetta.rosetta.core.pack.task.operation) TaskOperationFactory (class in pyrosetta.rosetta.core.pack.task.operation) TaskOperationFeatures (class in pyrosetta.rosetta.protocols.features) TaskOperationFeatures.Taskop_id_name_factory_ (class in pyrosetta.rosetta.protocols.features) TaskOperationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) TaskOperationLoader (class in pyrosetta.rosetta.protocols.parser) TaskOperationLoaderCreator (class in pyrosetta.rosetta.protocols.parser) TaskOperationMPM (class in pyrosetta.rosetta.protocols.match) tasks() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) TaskSelector (class in pyrosetta.rosetta.protocols.residue_selectors) TaskSelectorCreator (class in pyrosetta.rosetta.protocols.residue_selectors) tau_angles (pyrosetta.rosetta.core.chemical.rings.RingConformer property) TAU_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) TAUTOMER (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) tautomerize_anomer() (in module pyrosetta.rosetta.core.pose.carbohydrates) TautomerizeAnomerMover (class in pyrosetta.rosetta.protocols.carbohydrates) TautomerizeAnomerMoverCreator (class in pyrosetta.rosetta.protocols.carbohydrates) Tb (pyrosetta.rosetta.core.chemical.element.Elements attribute) TB3_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) TBMB (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) TBMB_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) Tc (pyrosetta.rosetta.core.chemical.element.Elements attribute) tcp_main() (in module pyrosetta.network.rosetta_udp_to_tcp_bridge) tcr_graft_model() (pyrosetta.rosetta.protocols.tcr.TCRmodel method) tcr_loop_model() (pyrosetta.rosetta.protocols.tcr.TCRloopRefine method) (pyrosetta.rosetta.protocols.tcr.TCRmodel method) tcr_model() (pyrosetta.rosetta.protocols.tcr.TCRmodel method) TCRloopRefine (class in pyrosetta.rosetta.protocols.tcr) TCRmodel (class in pyrosetta.rosetta.protocols.tcr) TCRmodel.tcrtmplts (class in pyrosetta.rosetta.protocols.tcr) TCRmodel.tmpltinfo (class in pyrosetta.rosetta.protocols.tcr) TCRseqInfo (class in pyrosetta.rosetta.protocols.tcr) TCRseqInfo.tcrposi (class in pyrosetta.rosetta.protocols.tcr) TCRseqInfo.tcrsegs (class in pyrosetta.rosetta.protocols.tcr) tdb (pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo property) Te (pyrosetta.rosetta.core.chemical.element.Elements attribute) tearDown() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) tearDownClass() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO class method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor class method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor class method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor class method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent class method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs class method) tell_neighbors_to_prep_for_relaxation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) tellg() (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) tellp() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t method) (pyrosetta.rosetta.basic.ComparingTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerToFile method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.std.ostream method) (pyrosetta.rosetta.std.ostringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wostream method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) temp (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) temp() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.protocols.multistate_design.PartitionAggregateFunction method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) temp0 (pyrosetta.rosetta.protocols.md.MDscheduleData property) temp0() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase 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_coords_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) 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) temp_final() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) temp_id() (pyrosetta.rosetta.protocols.moves.SimulatedTempering method) temp_initial() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) temperature (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.pose.PDBInfo.AtomRecord property) (pyrosetta.rosetta.protocols.ligand_docking.Transform_info property) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info property) temperature() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange 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.loops.loop_closure.ccd.RamaCheck1B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.moves.SimulatedTempering method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover 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) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) temperature_level() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange 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.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange 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.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) TemperedDocking (class in pyrosetta.rosetta.protocols.docking) TemperedDockingCreator (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) templ() (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) templ_selector() (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) templ_target() (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) Template (class in pyrosetta.rosetta.protocols.abinitio) template_atom_inds() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) template_file() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) template_from_res() (pyrosetta.rosetta.protocols.splice.SpliceManager method) TEMPLATE_HYBRIDIZATION_HISTORY (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) template_index() (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) template_insertion_ranges() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) template_label() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) template_name() (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) template_number() (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) template_pdb_fname() (pyrosetta.rosetta.protocols.splice.RBOutMover method) template_pose() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) template_poses() (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) template_res_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) template_res_cache_size() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) template_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) template_size() (pyrosetta.rosetta.protocols.jumping.MembraneJump method) template_stem1() (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) template_stem2() (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) template_to_res() (pyrosetta.rosetta.protocols.splice.SpliceManager method) template_to_unfolded_mapping() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) TemplateFragmentClaimer (class in pyrosetta.rosetta.protocols.topology_broker) TemplateHistory (class in pyrosetta.rosetta.protocols.hybridization) TemplateJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) TemplateJumpSetup (class in pyrosetta.rosetta.protocols.abinitio) Templates (class in pyrosetta.rosetta.protocols.abinitio) 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) ten_A_neighbor_graph (pyrosetta.rosetta.core.scoring.ContextGraphType attribute) tenA_neighbor_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) TenANeighborEdge (class in pyrosetta.rosetta.core.scoring) TenANeighborGraph (class in pyrosetta.rosetta.core.scoring) TenANeighborNode (class in pyrosetta.rosetta.core.scoring) tensor() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) tensor_fixed() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) tensor_name() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) tensors_fixed() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) TensorsOptimizer (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) TensorsOptimizer_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) TensorsOptimizer_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) TensorsOptimizer_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) TensorsOptimizer_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) TensorsOptimizerFix (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) TensorsOptimizerSvd (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) TER (pyrosetta.rosetta.core.io.pdb.RecordType attribute) terCount (pyrosetta.rosetta.core.io.AtomInformation property) terCount() (pyrosetta.rosetta.core.io.ResidueInformation method) term_length() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) term_w_bb (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) term_w_cycle (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) term_w_start (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) terminal_pair() (pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver method) terminal_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) TerminalDSSPSortedPoseVector (class in pyrosetta.rosetta.protocols.pose_sewing.data_storage) termini() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) termini_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) TerminiConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) TerminiConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) Terminus (class in pyrosetta.rosetta.core.pose.rna) TERMINUS (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) terminus() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove method) terminus_motif_score() (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) TerminusDistanceFilter (class in pyrosetta.rosetta.protocols.simple_filters) TerminusDistanceFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) TerminusMotifScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) TerminusMotifScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) TERPENE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) test() (in module pyrosetta.tests) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandAssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) (pyrosetta.rosetta.protocols.toolbox.DummyClass method) TEST1 (pyrosetta.rosetta.basic.ProfTag attribute) TEST2 (pyrosetta.rosetta.basic.ProfTag attribute) TEST3 (pyrosetta.rosetta.basic.ProfTag attribute) TEST4 (pyrosetta.rosetta.basic.ProfTag attribute) TEST5 (pyrosetta.rosetta.basic.ProfTag attribute) test_AA() (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) test_all_mg_hydration_frames() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) test_all_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) test_chunk() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) test_count_one (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) test_count_two (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) test_flexbb_rotamer_sets() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) test_for_stage_end() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) test_if_schema_is_valid() (in module pyrosetta.rosetta.utility.tag) test_labels() (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) test_loop_sample() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) test_move() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) test_p() (pyrosetta.rosetta.utility.py.OverloadTest method) test_pose_io() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) test_poses_to_silent() (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) test_ref() (pyrosetta.rosetta.utility.py.OverloadTest method) test_res_res_aln() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) test_residues() (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) test_round() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) test_saving_library() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) test_scores() (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) test_worker_extra() (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) testCartesianDerivatives() (pyrosetta.rosetta.protocols.cartesian.MolecularDynamics method) TestCompositeRealMetric (class in pyrosetta.rosetta.core.simple_metrics) TestCompositeRealMetricCreator (class in pyrosetta.rosetta.core.simple_metrics) TestCompositeStringMetric (class in pyrosetta.rosetta.core.simple_metrics) TestCompositeStringMetricCreator (class in pyrosetta.rosetta.core.simple_metrics) TestDaskArgs (class in pyrosetta.tests.distributed.test_dask_worker) testNeighbor() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) TestPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) TestPerResidueProbabilitiesMetric (class in pyrosetta.rosetta.core.simple_metrics) TestPerResidueProbabilitiesMetricCreator (class in pyrosetta.rosetta.core.simple_metrics) TestPerResidueRealMetric (class in pyrosetta.rosetta.core.simple_metrics) TestPerResidueRealMetricCreator (class in pyrosetta.rosetta.core.simple_metrics) TestPerResidueStringMetric (class in pyrosetta.rosetta.core.simple_metrics) TestPerResidueStringMetricCreator (class in pyrosetta.rosetta.core.simple_metrics) TestPoseIO (class in pyrosetta.tests.bindings.core.test_pose) TestPoseResidueAccessor (class in pyrosetta.tests.bindings.core.test_pose) TestPoseResidueLabelAccessor (class in pyrosetta.tests.bindings.core.test_pose) TestPoseScoresAccessor (class in pyrosetta.tests.bindings.core.test_pose) TestPosesToSilent (class in pyrosetta.tests.bindings.core.test_pose) TestRealMetric (class in pyrosetta.rosetta.core.simple_metrics) TestRealMetricCreator (class in pyrosetta.rosetta.core.simple_metrics) TestStringMetric (class in pyrosetta.rosetta.core.simple_metrics) TestStringMetricCreator (class in pyrosetta.rosetta.core.simple_metrics) tether_jump() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) tether_ligand_ (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) tether_to_closest_res() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.SampleGrid method) TetherLigand (class in pyrosetta.rosetta.protocols.ligand_docking) TETRAGONAL (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting attribute) tetrahedral_metal (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) TetrahedralMetal_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) TETRALOOP_TL_RECEPTOR (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) TETROSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) tf (pyrosetta.rosetta.protocols.features.TaskOperationFeatures.Taskop_id_name_factory_ property) tf_constant (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction attribute) tf_end_of_list (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction attribute) tf_linear (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction attribute) tf_quadratic (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction attribute) tf_unknown (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction attribute) (pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction attribute) TFDataTypeDetector_bool_t (class in pyrosetta.rosetta.basic.tensorflow_manager) TFDataTypeDetector_double_t (class in pyrosetta.rosetta.basic.tensorflow_manager) TFDataTypeDetector_float_t (class in pyrosetta.rosetta.basic.tensorflow_manager) TFDataTypeDetector_int_t (class in pyrosetta.rosetta.basic.tensorflow_manager) TFDataTypeDetector_long_t (class in pyrosetta.rosetta.basic.tensorflow_manager) TFDataTypeDetector_unsigned_int_t (class in pyrosetta.rosetta.basic.tensorflow_manager) TFDataTypeDetector_unsigned_long_t (class in pyrosetta.rosetta.basic.tensorflow_manager) Th (pyrosetta.rosetta.core.chemical.element.Elements attribute) then_expression() (pyrosetta.rosetta.numeric.expression_parser.ITEExpression method) THEORETICAL_MODEL (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) TheozymeInvrotTree (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) THERMAL_SAMPLER (pyrosetta.rosetta.protocols.stepwise.modeler.MinimizerMode attribute) thermal_sampler_mode() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) thermal_sampler_output_min_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) thermal_sampler_temperature() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) ThermalMinimizer (class in pyrosetta.rosetta.protocols.recces.scratch) ThermalMinimizerCreator (class in pyrosetta.rosetta.protocols.recces.scratch) ThermalSamplingMover (class in pyrosetta.rosetta.protocols.recces.scratch) ThermalSamplingMoverCreator (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) Thermostat (class in pyrosetta.rosetta.protocols.md) THETA (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) (pyrosetta.rosetta.core.id.DOF_Type attribute) theta() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) theta0() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) THETA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) thickness (pyrosetta.rosetta.core.conformation.membrane.MEM attribute) thickness() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) thickness_ (pyrosetta.rosetta.core.scoring.packstat.Slice property) Thio (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) THIO_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) thioether (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) Thioether_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) Thioredoxin (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) this_aa() (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData method) thole() (pyrosetta.rosetta.core.scoring.MultipoleParameter method) thread() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) thread_ids (pyrosetta.rosetta.basic.thread_manager.RosettaThreadAllocation property) thread_limit() (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation method) thread_manager_initialization_begun() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManagerInitializationTracker method) thread_manager_was_initialized() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManagerInitializationTracker method) thread_original_sequence() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) thread_seq() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter 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) ThreadingJobInputterCreator (class in pyrosetta.rosetta.protocols.comparative_modeling) ThreadingMover (class in pyrosetta.rosetta.protocols.comparative_modeling) ThreadSequenceOperation (class in pyrosetta.rosetta.protocols.task_operations) ThreadSequenceOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) three_body_approximate_buried_unsat_calculation() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty) three_fold (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) three_letter_code() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) THREE_PRIME (pyrosetta.rosetta.core.pose.rna.Terminus attribute) three_prime_atom (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point property) THREE_PRIME_AZIDE (pyrosetta.rosetta.core.chemical.VariantType attribute) three_prime_chain_break_res() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker method) THREE_PRIME_DEOXY (pyrosetta.rosetta.core.chemical.VariantType attribute) THREE_PRIME_END_OH (pyrosetta.rosetta.core.chemical.VariantType attribute) THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) THREE_PRIME_PACKABLE_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) THREE_PRIME_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus attribute) three_prime_seq_num (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point property) THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) THREEDGRID (pyrosetta.rosetta.core.conformation.Strategy attribute) THREELETTER_CODE (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode attribute) THRESHOLD (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) threshold() (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.MatchResidues method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) threshold_probability() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) thresholds() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) throw_sm_override_error() (in module pyrosetta.rosetta.core.simple_metrics) Ti (pyrosetta.rosetta.core.chemical.element.Elements attribute) tid (pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo property) 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) tightness() (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) tilt() (pyrosetta.rosetta.protocols.dna.DNABasestep 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_minobj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) time_pts() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) time_to_checkpoint() (pyrosetta.rosetta.protocols.checkpoint.Timer static method) TimeEvaluator (class in pyrosetta.rosetta.protocols.evaluation) TimeFilter (class in pyrosetta.rosetta.protocols.filters) TimeFilterCreator (class in pyrosetta.rosetta.protocols.filters) Timer (class in pyrosetta.rosetta.basic.gpu) (class in pyrosetta.rosetta.protocols.checkpoint) Times() (pyrosetta.rosetta.basic.sampling.orientations.Quaternion method) timestamp (pyrosetta.rosetta.basic.TracerOptions property) timestamp() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) timestamp_millis() (in module pyrosetta.rosetta.utility) timestamp_millis_short() (in module pyrosetta.rosetta.utility) timestamp_short() (in module pyrosetta.rosetta.utility) TimingProfileMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) TimingProfileMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) TITLE (pyrosetta.rosetta.core.io.pdb.RecordType attribute) title (pyrosetta.rosetta.protocols.relax.DatabaseRelaxScript property) title() (pyrosetta.rosetta.core.io.HeaderInformation method) title_width() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) titrate_stack_bonus() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) Tl (pyrosetta.rosetta.core.chemical.element.Elements attribute) TL_RECEPTOR (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) tm (class in pyrosetta.rosetta) Tm (pyrosetta.rosetta.core.chemical.element.Elements attribute) TM (pyrosetta.rosetta.core.scoring.TMscoreStore property) TM10 (pyrosetta.rosetta.core.scoring.TMscoreStore property) TM10_max (pyrosetta.rosetta.core.scoring.TMscoreStore property) TM3_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) tm_gmtoff (pyrosetta.rosetta.tm property) tm_hour (pyrosetta.rosetta.tm property) tm_isdst (pyrosetta.rosetta.tm property) TM_max (pyrosetta.rosetta.core.scoring.TMscoreStore property) tm_mday (pyrosetta.rosetta.tm property) tm_min (pyrosetta.rosetta.tm property) tm_mon (pyrosetta.rosetta.tm property) tm_projection_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) tm_sec (pyrosetta.rosetta.tm property) TM_sum (pyrosetta.rosetta.core.scoring.TMscoreStore property) TM_sum10 (pyrosetta.rosetta.core.scoring.TMscoreStore property) tm_wday (pyrosetta.rosetta.tm property) tm_yday (pyrosetta.rosetta.tm property) tm_year (pyrosetta.rosetta.tm property) TMA (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) TMA_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) TMalign (class in pyrosetta.rosetta.protocols.hybridization) tmh_inserted() (pyrosetta.rosetta.core.scoring.MembraneTopology method) tmhelix() (pyrosetta.rosetta.core.scoring.MembraneTopology method) TMHTopologySamplerClaimer (class in pyrosetta.rosetta.protocols.topology_broker) 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) tmregion() (pyrosetta.rosetta.core.scoring.MembraneTopology method) TMsAACompFilter (class in pyrosetta.rosetta.protocols.simple_filters) TMsAACompFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) TMscore (class in pyrosetta.rosetta.core.scoring) TMscore() (pyrosetta.rosetta.protocols.hybridization.TMalign method) TMscore8_search() (pyrosetta.rosetta.protocols.hybridization.TMalign method) TMscoreStore (class in pyrosetta.rosetta.core.scoring) TMsSpanMembraneFilter (class in pyrosetta.rosetta.protocols.simple_filters) TMsSpanMembraneFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) TNA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) tna_suite (pyrosetta.rosetta.core.scoring.ScoreType attribute) tna_suite_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) TNA_SuiteEnergy (class in pyrosetta.rosetta.core.energy_methods) TNA_SuiteEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) TNA_SuitePotential (class in pyrosetta.rosetta.core.scoring.rna) to_all_atom() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol 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.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) to_chain() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) to_default() (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) to_degrees() (in module pyrosetta.rosetta.numeric.conversions) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) to_diag() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) to_dict() (in module pyrosetta.distributed.packed_pose.core) to_do() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) to_entry() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) (pyrosetta.rosetta.protocols.splice.RBInMover method) to_identity() (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) to_left() (in module pyrosetta.rosetta.core.membrane) to_local_coordinate() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) to_local_name() (pyrosetta.rosetta.utility.file.FileName method) to_minipose() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) to_multichain_pose() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) to_output_record() (in module pyrosetta.distributed.io) to_packed() (in module pyrosetta.distributed.packed_pose.core) to_pdbstring() (in module pyrosetta.distributed.io) to_pose() (in module pyrosetta.distributed.packed_pose.core) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) to_pose_from_db() (pyrosetta.rosetta.protocols.legacy_sewing.Model method) to_quaternion() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) to_radians() (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) to_res() (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.splice.Splice method) to_silent() (in module pyrosetta.distributed.io) 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.id.SequenceMapping method) (pyrosetta.rosetta.core.io.mmtf.sd_index method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.numeric.expression_parser.FunctionToken method) (pyrosetta.rosetta.numeric.expression_parser.LiteralToken method) (pyrosetta.rosetta.numeric.expression_parser.SimpleToken method) (pyrosetta.rosetta.numeric.expression_parser.Token method) (pyrosetta.rosetta.numeric.expression_parser.VariableToken method) (pyrosetta.rosetta.numeric.kdtree.KDPoint method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) (pyrosetta.rosetta.protocols.multistate_design.PosType method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.utility.tag.Tag method) toFloat() (in module pyrosetta.rosetta.protocols.cluster.calibur) toggle() (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim method) toInt() (in module pyrosetta.rosetta.protocols.cluster.calibur) Token (class in pyrosetta.rosetta.numeric.expression_parser) token (pyrosetta.rosetta.protocols.jd3.dag_node_managers.ResultElements property) 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) TokenSet (class in pyrosetta.rosetta.numeric.expression_parser) TokenType (class in pyrosetta.rosetta.numeric.expression_parser) tol() (pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc method) tolerance() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D 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.toolbox.match_enzdes_util.GeomSampleInfo method) tolerated_overlap() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) too_far() (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) ToolboxKeys (class in pyrosetta.rosetta.protocols.loop_modeling) top() (pyrosetta.rosetta.numeric.expression_parser.TokenSet method) (pyrosetta.rosetta.protocols.dna.DnaPosition method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareByScoreCombination_t method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.std.priority_queue_protocols_motif_grafting_movers_MotifMatch_std_vector_protocols_motif_grafting_movers_MotifMatch_std_less_protocols_motif_grafting_movers_MotifMatch_t method) Top7 (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) top_fragments() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) top_level_pool_size() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) TopCountOfAllInputs (class in pyrosetta.rosetta.protocols.features) TopCountOfEachInput (class in pyrosetta.rosetta.protocols.features) TopEntitySet (class in pyrosetta.rosetta.protocols.pack_daemon) TopNByProperty (class in pyrosetta.rosetta.protocols.pose_selectors) TopNByPropertyCreator (class in pyrosetta.rosetta.protocols.pose_selectors) TopNMotifScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) TopNMotifScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) topNtrans_ (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) TOPO_RESAMPLING (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom.IterationStage attribute) 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() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) topology_broker() (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) topology_score() (pyrosetta.rosetta.protocols.abinitio.Template method) TopologyBroker (class in pyrosetta.rosetta.protocols.topology_broker) TopologyBrokerMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) TopologyBrokerMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) TopologyClaimer (class in pyrosetta.rosetta.protocols.topology_broker) TopologyClaimerFactory (class in pyrosetta.rosetta.protocols.topology_broker) TopOutFunc (class in pyrosetta.rosetta.core.scoring.func) TopPercentOfAllInputs (class in pyrosetta.rosetta.protocols.features) TopPercentOfEachInput (class in pyrosetta.rosetta.protocols.features) tor1 (pyrosetta.rosetta.protocols.normalmode.ContactStruct property) tor2 (pyrosetta.rosetta.protocols.normalmode.ContactStruct property) tor_for_dof() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) tor_U1D3 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleConstraint property) tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) tor_U2D2 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleConstraint property) tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) tor_U3D1 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleConstraint property) tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) Torsion (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) torsion (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo property) 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.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.normalmode.NormalMode method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) torsion2big_bin() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionFeature static method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerRecovery method) 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) torsion_angle_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) torsion_bin() (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionFeature method) torsion_changes_move_other_monomers() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo 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 static method) torsion_database() (pyrosetta.rosetta.protocols.splice.Splice method) torsion_database_fname() (pyrosetta.rosetta.protocols.splice.Splice 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) torsion_id() (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) torsion_id_ranges() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover 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.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) torsion_in_align() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner method) Torsion_Info (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) torsion_is_independent() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) torsion_name() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) torsion_parameters() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) torsion_potential() (pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions method) torsion_sample_value() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) torsion_scale_factor() (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) torsion_source_name (pyrosetta.rosetta.core.fragment.rna.TorsionSet property) torsion_type() (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) torsional_derivative_from_cartesian_derivatives() (in module pyrosetta.rosetta.core.optimization) TorsionBin (class in pyrosetta.rosetta.protocols.comparative_modeling.features) TorsionBinIO (class in pyrosetta.rosetta.protocols.frag_picker) TorsionBinSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) TorsionClaim (class in pyrosetta.rosetta.protocols.environment.claims) TorsionCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) TorsionDistrParams (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) TorsionDOFMover (class in pyrosetta.rosetta.protocols.simple_moves) TorsionEnergy (class in pyrosetta.rosetta.core.pack.rotamers) TorsionFeature (class in pyrosetta.rosetta.protocols.comparative_modeling.features) TorsionFourierComponent (class in pyrosetta.rosetta.core.scoring.dna) TorsionFragment (class in pyrosetta.rosetta.protocols.frags) TorsionFragmentLibrary (class in pyrosetta.rosetta.protocols.frags) TorsionFragmentMover (class in pyrosetta.rosetta.protocols.frags) TorsionID (class in pyrosetta.rosetta.core.id) TorsionID_Range (class in pyrosetta.rosetta.core.id) TorsionParams (class in pyrosetta.rosetta.core.scoring) TorsionPerturbType (class in pyrosetta.rosetta.protocols.simple_moves) TorsionRange (class in pyrosetta.rosetta.protocols.make_rot_lib) TorsionRestrictedKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) torsions (class in pyrosetta.rosetta.core.fragment) (pyrosetta.rosetta.core.fragment.rna.TorsionSet property) torsions() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) TorsionSampler (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) TorsionSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) TorsionSet (class in pyrosetta.rosetta.core.fragment.rna) TorsionSetMover (class in pyrosetta.rosetta.protocols.simple_moves) torsionsMCM (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) TorsionSpec (class in pyrosetta.rosetta.protocols.canonical_sampling) TorsionSpecStyle (class in pyrosetta.rosetta.protocols.canonical_sampling) TorsionSweepingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) TorsionType (class in pyrosetta.rosetta.core.id) (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) tot (pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy property) tot_rotamer_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) tot_score() (pyrosetta.rosetta.core.scoring.motif.XformScore method) tot_surf (pyrosetta.rosetta.core.scoring.packing.SurfVol property) (pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv property) tot_vol (pyrosetta.rosetta.core.scoring.packing.SurfVol property) (pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv property) TOTAL (pyrosetta.rosetta.basic.ProfTag attribute) total (pyrosetta.rosetta.protocols.analysis.InterfaceRegion attribute) total() (pyrosetta.rosetta.core.scoring.saxs.DistanceHistogram method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator method) total_accepts() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) total_area (pyrosetta.rosetta.core.scoring.packstat.AreaAccumulator property) total_atoms() (pyrosetta.rosetta.core.pose.Pose method) total_bin (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) total_buried_volume() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) total_chain_break_score (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) total_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count property) total_counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) total_embed() (pyrosetta.rosetta.protocols.membrane.geometry.Embedding method) total_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) total_energies_array() (in module pyrosetta.bindings.energies) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) total_energies_weighted() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) total_energy() (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (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.loop_graph.LoopGraph method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) total_energy_from_pose() (in module pyrosetta.rosetta.core.pose) total_hb_E (pyrosetta.rosetta.protocols.analysis.InterfaceData property) total_hbonds (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) total_helices (pyrosetta.rosetta.core.scoring.Helices property) total_HH_dimer (pyrosetta.rosetta.core.scoring.Helices property) total_net_change_in_rama_score_over_range() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase method) total_nr_jobs() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) TOTAL_NUM_CRITERIA (pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType attribute) total_number_abego() (pyrosetta.rosetta.core.sequence.ABEGOManager method) total_number_elements (pyrosetta.rosetta.core.chemical.element.Elements attribute) total_polar_atoms (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) total_proposed() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) total_residue() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets 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.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.trie.TrieCollection method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) (pyrosetta.rosetta.protocols.jumping.JumpSample 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.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.parser.BluePrint method) total_residue_wolig() (pyrosetta.rosetta.protocols.parser.BluePrint method) total_score (pyrosetta.rosetta.core.scoring.motif.MotifHits property) (pyrosetta.rosetta.core.scoring.ScoreType attribute) 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.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC 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_SS_dimer (pyrosetta.rosetta.core.scoring.Strands property) total_standard_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) total_strands (pyrosetta.rosetta.core.scoring.Strands property) total_threads() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManager static method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManagerInitializationTracker method) total_trials() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) TotalEnergyMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) TotalEnergyMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) TotalSasaFilter (class in pyrosetta.rosetta.protocols.simple_filters) TotalSasaFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) TotalScoreFeatures (class in pyrosetta.rosetta.protocols.features) TotalScoreFeaturesCreator (class in pyrosetta.rosetta.protocols.features) tournament_select() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) TP3 (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) tpdb (pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo property) tpiece (pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo property) trace (class in pyrosetta.rosetta.core.scoring.packstat) Trace (pyrosetta.rosetta.basic.MemTracer property) (pyrosetta.rosetta.basic.MemTracerImpl property) (pyrosetta.rosetta.basic.Tracer property) (pyrosetta.rosetta.basic.TracerImpl property) trace() (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) trace_from_distr() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) traceback() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.sequence.Aligner method) (pyrosetta.rosetta.core.sequence.MCAligner method) (pyrosetta.rosetta.core.sequence.NWAligner method) (pyrosetta.rosetta.core.sequence.SWAligner method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) Tracer (class in pyrosetta.rosetta.basic) tracer() (pyrosetta.rosetta.protocols.rpc.JSON_RPC method) Tracer.TracerProxy (class in pyrosetta.rosetta.basic) TracerImpl (class in pyrosetta.rosetta.basic) TracerImpl.sentry (class in pyrosetta.rosetta.basic) TracerImpl.TracerProxyImpl (class in pyrosetta.rosetta.basic) TracerImpl.TracerProxyImpl.sentry (class in pyrosetta.rosetta.basic) TracerOptions (class in pyrosetta.rosetta.basic) TracerPriority (class in pyrosetta.rosetta.basic) TracerToFile (class in pyrosetta.rosetta.basic) TracerToFile.sentry (class in pyrosetta.rosetta.basic) traces_ (pyrosetta.rosetta.core.scoring.packstat.Slice property) track_completed_job() (pyrosetta.rosetta.protocols.jd3.JobTracker method) track_deallocated_input_pose() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) track_job_completed() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) track_job_node_assigned() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) track_job_node_being_assigned() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) track_starting_job_list() (pyrosetta.rosetta.protocols.jd3.JobTracker method) TRADITIONAL_MINIMIZER (pyrosetta.rosetta.protocols.stepwise.modeler.MinimizerMode attribute) train() (pyrosetta.rosetta.core.scoring.func.CircularSplineFunc method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_1_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_2_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_3_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_4_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_5_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_6_t method) traits() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) traits_string() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) trajectory_file_name() (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) Trajectory_state (pyrosetta.rosetta.protocols.viewer.GraphicsState property) TrajectoryLogger (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) TrajectoryMapFeatures (class in pyrosetta.rosetta.protocols.features) TrajectoryMapFeaturesCreator (class in pyrosetta.rosetta.protocols.features) TrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) TrajectoryReportToDB (class in pyrosetta.rosetta.protocols.features) TrajectoryReportToDBCreator (class in pyrosetta.rosetta.protocols.features) TrajectoryState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) TRANS (pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation attribute) trans() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) 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.enzdes.PredesignPerturbMover method) (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) TRANS_X (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric attribute) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric.DOF attribute) TRANS_Y (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric attribute) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric.DOF attribute) TRANS_Z (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric attribute) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric.DOF attribute) transaction (class in pyrosetta.rosetta.cppdb) (class in pyrosetta.rosetta.utility.sql_database) transaction_mode_from_name() (in module pyrosetta.rosetta.utility.sql_database) TransactionMode (class in pyrosetta.rosetta.utility.sql_database) TransactionMode.e (class in pyrosetta.rosetta.utility.sql_database) TRANSFER (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) transfer_constraint_set() (pyrosetta.rosetta.core.pose.Pose method) transfer_jumps() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.jumping.JumpSample method) transfer_phi_psi() (in module pyrosetta.rosetta.core.pose) transfer_unfolded_conformation() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) Transform (class in pyrosetta.rosetta.protocols.ligand_docking) transform() (pyrosetta.rosetta.core.conformation.UltraLightResidue method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternTransform method) (pyrosetta.rosetta.protocols.hybridization.TMalign method) (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_info (class in pyrosetta.rosetta.protocols.ligand_docking) transform_ligand() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) transform_model() (pyrosetta.rosetta.protocols.legacy_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_pose() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) transform_res_to_subunit() (in module pyrosetta.rosetta.protocols.loop_grower) transform_sap_to_score() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) transform_segment_coords() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) transform_segments() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) transform_to_closest_symmunit() (in module pyrosetta.rosetta.protocols.loop_grower) Transformation (class in pyrosetta.rosetta.protocols.protein_interface_design) TransformCreator (class in pyrosetta.rosetta.protocols.ligand_docking) TransformEnsemble (class in pyrosetta.rosetta.protocols.ligand_docking) TransformEnsemble_info (class in pyrosetta.rosetta.protocols.ligand_docking) TransformEnsembleCreator (class in pyrosetta.rosetta.protocols.ligand_docking) 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) TransientCutpointHandler (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) transition_threshold() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) transitive_map() (in module pyrosetta.rosetta.core.sequence) Translate (class in pyrosetta.rosetta.protocols.ligand_docking) translate() (in module pyrosetta.bindings.pose) (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) (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) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) translate_index (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) Translate_info (class in pyrosetta.rosetta.protocols.ligand_docking) translate_ligand() (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) translate_virt_to_CoM() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) translate_virtual_anchor_to_first_rigid_body() (in module pyrosetta.rosetta.protocols.rna.denovo) TranslateCreator (class in pyrosetta.rosetta.protocols.ligand_docking) translateDSSP_ABEGO() (pyrosetta.rosetta.protocols.forge.remodel.RemodelData method) translation (pyrosetta.rosetta.protocols.protein_interface_design.Transformation property) translation() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float_t method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.sic_dock.xyzStripeHashPoseWithMeta method) translation_ (pyrosetta.rosetta.protocols.loop_grower.SheetPositions property) translation_along_axis() (pyrosetta.rosetta.core.kinematics.Jump method) translation_real() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash 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() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) transpose_product() (in module pyrosetta.rosetta.numeric) transpose_so3() (in module pyrosetta.rosetta.numeric.fourier) transposed() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) transposeRowSize() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) treat_AND_and_OR_as_operators() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticScanner method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionScanner method) treat_NOT_as_operator() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticScanner method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionScanner method) tree() (pyrosetta.rosetta.numeric.kdtree.KDNode method) tree_from_jumps_and_cuts() (pyrosetta.rosetta.core.kinematics.FoldTree method) tree_init() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) tree_type() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) triage_filter() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) triage_threshold() (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) trial() (pyrosetta.rosetta.protocols.moves.TrialCounter method) trial_counter() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) TrialCounter (class in pyrosetta.rosetta.protocols.moves) 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.monte_carlo) triangle (class in pyrosetta.rosetta.protocols.viewer) triangleIterator (class in pyrosetta.rosetta.protocols.viewer) TRIAZOLAMERC (pyrosetta.rosetta.core.chemical.VariantType attribute) TriazolamerMover (class in pyrosetta.rosetta.protocols.simple_moves.triazolamer) TRIAZOLAMERN (pyrosetta.rosetta.core.chemical.VariantType attribute) TriazolamerRandomSmallMover (class in pyrosetta.rosetta.protocols.simple_moves.triazolamer) TRIAZOLE_LINKER (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) TRICLINIC (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting attribute) TricubicSpline (class in pyrosetta.rosetta.numeric.interpolation.spline) trie() (pyrosetta.rosetta.core.scoring.trie.TrieCollection method) trie_vs_path() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) trie_vs_trie() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) TrieCollection (class in pyrosetta.rosetta.core.scoring.trie) TrieCountPair1BC3 (class in pyrosetta.rosetta.core.scoring.etable.etrie) TrieCountPair1BC4 (class in pyrosetta.rosetta.core.scoring.etable.etrie) TrieCountPairAll (class in pyrosetta.rosetta.core.scoring.etable.etrie) TrieCountPairBase (class in pyrosetta.rosetta.core.scoring.trie) TrieCountPairGeneric (class in pyrosetta.rosetta.core.scoring.etable.etrie) TrieCountPairNone (class in pyrosetta.rosetta.core.scoring.etable.etrie) tries() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) TrieVsTrieCachedDataContainerBase (class in pyrosetta.rosetta.core.scoring.trie) trigger_accept() (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) trigonal_planar_metal (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) trigonal_pyramidal_metal (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) TrigonalPlanarMetal_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) TrigonalPyramidalMetal_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) 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 static method) trim_additional_rotamers() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) trim_back_sequence_mapping() (in module pyrosetta.rosetta.protocols.loops) trim_based_on_known_ligand() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) trim_chunks() (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) trim_cter() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) trim_db_pose() (pyrosetta.rosetta.protocols.legacy_sewing.Model method) trim_framework() (in module pyrosetta.rosetta.protocols.antibody.grafting) trim_neighbors_by_distance() (in module pyrosetta.rosetta.core.select) trim_pose() (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) trim_scores() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) trim_terminal_segments() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) trim_to_heterogeneous_clusters() (pyrosetta.rosetta.protocols.simple_moves.AtomHash 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) TRIMETHYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) trimFiberDiffractionData() (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffraction 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 static 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) TRIOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) tripFileName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) Triple (class in pyrosetta.rosetta.basic.sampling.orientations) triple_constel_set() (in module pyrosetta.rosetta.protocols.constel) triple_constel_set_idx3() (in module pyrosetta.rosetta.protocols.constel) TripleBond (pyrosetta.rosetta.core.chemical.BondName attribute) TripleBondOrder (pyrosetta.rosetta.core.chemical.BondOrder attribute) triplet_and_originnum (class in pyrosetta.rosetta.protocols.pockets) triplet_fingerprint_data() (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) TRIPLET_Tab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) TripletID (class in pyrosetta.rosetta.protocols.fldsgn.topology) TrisBpyScore (class in pyrosetta.rosetta.protocols.sic_dock.scores) trj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) trj_score_only() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) trj_scratch() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) trRosettaConstraintGenerator (class in pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators) trRosettaConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators) trRosettaOutputs_v1 (class in pyrosetta.rosetta.protocols.trRosetta) trRosettaOutputsBase (class in pyrosetta.rosetta.protocols.trRosetta) trRosettaProtocol_v1 (class in pyrosetta.rosetta.protocols.trRosetta) trRosettaProtocolBackboneMinimizationMode (class in pyrosetta.rosetta.protocols.trRosetta_protocols.movers) trRosettaProtocolBackboneRandomizationMode (class in pyrosetta.rosetta.protocols.trRosetta_protocols.movers) trRosettaProtocolBase (class in pyrosetta.rosetta.protocols.trRosetta) trRosettaProtocolMover (class in pyrosetta.rosetta.protocols.trRosetta_protocols.movers) trRosettaProtocolMoverCreator (class in pyrosetta.rosetta.protocols.trRosetta_protocols.movers) True (pyrosetta.rosetta.utility.tag.AutoBool attribute) true_behavior() (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) true_negative (pyrosetta.rosetta.numeric.RocStatus attribute) true_positive (pyrosetta.rosetta.numeric.RocStatus attribute) trueD() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) TrueFalseFilter (class in pyrosetta.rosetta.protocols.filters) TrueFalseFilterCreator (class in pyrosetta.rosetta.protocols.filters) truefalseoption() (in module pyrosetta.rosetta.basic.options) TrueFilter (class in pyrosetta.rosetta.protocols.filters) TrueFilterCreator (class in pyrosetta.rosetta.protocols.filters) TrueResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) TrueResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) truncate_abego() (in module pyrosetta.rosetta.protocols.denovo_design.components) TRUNCATED_SCORE_EVALUATOR (pyrosetta.rosetta.basic.ProfTag attribute) TruncatedScoreEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) truncdomain (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs property) trust() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) 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) try_all_conformers() (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) try_all_pairs() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) try_elongating_helix() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) try_nucleating_helix() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) try_peptide_flip() (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) try_peptoid_flip() (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) try_perturbing_global_helix_parameters() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) try_perturbing_local_helix_parameters() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) try_point_mutants() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) try_pre_gly_flip() (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) try_retracting_helix() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) TryDisulfPermutations (class in pyrosetta.rosetta.protocols.cyclic_peptide) TryDisulfPermutationsCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) TryRotamers (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) TryRotamersCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) trytry_ifstream_open() (in module pyrosetta.rosetta.utility.file) trytry_ofstream_open() (in module pyrosetta.rosetta.utility.file) TS1_PSEUDOCONTACT_SHIFT_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) TS2_PSEUDOCONTACT_SHIFT_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) TS3_PSEUDOCONTACT_SHIFT_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) TS4_PSEUDOCONTACT_SHIFT_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) tscore (pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo property) tseq (pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo property) Tumble (class in pyrosetta.rosetta.protocols.simple_moves) TumbleCreator (class in pyrosetta.rosetta.protocols.simple_moves) turn_off_flank_relax() (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) turn_off_for_chunks() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) turn_off_H3_filter() (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) turn_off_h3_filter() (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) turn_off_repulsive_ramp() (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) turn_off_rna_chem_map_during_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) turn_on_benchmark() (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) tVal (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) TvecA (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) TvecB (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) twelve_A_neighbor_graph (pyrosetta.rosetta.core.scoring.ContextGraphType attribute) twelveA_neighbor_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) TwelveANeighborEdge (class in pyrosetta.rosetta.core.scoring) TwelveANeighborGraph (class in pyrosetta.rosetta.core.scoring) TwelveANeighborNode (class in pyrosetta.rosetta.core.scoring) twiddles() (pyrosetta.rosetta.numeric.fourier.kiss_fft_state method) twist() (pyrosetta.rosetta.protocols.dna.DNABasestep method) twist_level() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) Two (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) two() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) two_parts_chain1() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) two_step() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) twobody_energies() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) TwoBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) TwoDHistogram_unsigned_long_long_t (class in pyrosetta.rosetta.numeric.histograms) twoprime() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) TWOPRIME_RES (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) twoprime_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) type (pyrosetta.rosetta._xmlNode property) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.ResNum property) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) (pyrosetta.rosetta.core.scoring.sc._DOT property) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector.SSElement property) (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec property) (pyrosetta.rosetta.protocols.dna.PositionType property) (pyrosetta.rosetta.protocols.kinmatch.KRSQuery property) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo property) (pyrosetta.rosetta.protocols.md.MDscheduleData property) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.SSElement property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction property) (pyrosetta.rosetta.RDKit.RDValue property) type() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator 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.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.orbitals.OrbitalXYZCoords method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD 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.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.pose.rna.RNA_Reactivity method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.rna.RNA_Motif method) (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) (pyrosetta.rosetta.numeric.expression_parser.FunctionToken method) (pyrosetta.rosetta.numeric.expression_parser.LiteralToken method) (pyrosetta.rosetta.numeric.expression_parser.SimpleToken method) (pyrosetta.rosetta.numeric.expression_parser.Token method) (pyrosetta.rosetta.numeric.expression_parser.VariableToken method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.features.ResidueFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.SSFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.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.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect 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.HelixPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing 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.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.Contact method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.multistate_design.PosType method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.sic_dock.BuriedPolarScore method) (pyrosetta.rosetta.protocols.sic_dock.CBScore method) (pyrosetta.rosetta.protocols.sic_dock.ConstraintSetScore method) (pyrosetta.rosetta.protocols.sic_dock.EdgeStandScore method) (pyrosetta.rosetta.protocols.sic_dock.HelixScore method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.sic_dock.LinkerScore method) (pyrosetta.rosetta.protocols.sic_dock.RigidScore method) (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) (pyrosetta.rosetta.protocols.sic_dock.scores.TrisBpyScore method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentCost method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GunnCost method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) type1() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) type2() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) type_ (pyrosetta.rosetta.core.scoring.motif.MotifHash property) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop property) (pyrosetta.rosetta.protocols.hybridization.detailedControlsTagSetting property) type_for_fake_atoms() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) type_for_residuetype() (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory method) type_info (class in pyrosetta.rosetta.std) type_name() (pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeaturesCreator 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.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BatchFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProtocolFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.frag_picker.Contact 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.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirementCreator 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.loops.loops_definers.LoopsStringDefinerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSDCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiffCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiffCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBinsCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPackCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamersCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructureCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelaxCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrialsCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMinCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHumanCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimpleCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLiteCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement static method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer static 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_MODES_LENGTH (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) Type_to_type_bool_t (class in pyrosetta.rosetta.utility.json_spirit.internal_) Type_to_type_double_t (class in pyrosetta.rosetta.utility.json_spirit.internal_) Type_to_type_float_t (class in pyrosetta.rosetta.utility.json_spirit.internal_) Type_to_type_int_t (class in pyrosetta.rosetta.utility.json_spirit.internal_) Type_to_type_long_t (class in pyrosetta.rosetta.utility.json_spirit.internal_) Type_to_type_unsigned_long_t (class in pyrosetta.rosetta.utility.json_spirit.internal_) 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) TypeTraits_double_t (class in pyrosetta.rosetta.ObjexxFCL) TypeTraits_float_t (class in pyrosetta.rosetta.ObjexxFCL) TypeTraits_int_t (class in pyrosetta.rosetta.ObjexxFCL) TypeTraits_long_double_t (class in pyrosetta.rosetta.ObjexxFCL) TypeTraits_long_t (class in pyrosetta.rosetta.ObjexxFCL) TypeTraits_short_t (class in pyrosetta.rosetta.ObjexxFCL) TypeTraits_unsigned_int_t (class in pyrosetta.rosetta.ObjexxFCL) TypeTraits_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) TypeTraits_unsigned_short_t (class in pyrosetta.rosetta.ObjexxFCL) typGrid_ (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid property) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint property)