Index – S

s() (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.utility.py.Value method) s1_end() (pyrosetta.rosetta.core.scoring.Hairpin method) s1_start() (pyrosetta.rosetta.core.scoring.Hairpin method) s2_end() (pyrosetta.rosetta.core.scoring.Hairpin method) s2_start() (pyrosetta.rosetta.core.scoring.Hairpin method) s2d() (pyrosetta.rosetta.utility.subset_mapping method) sa() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) sa_faraggi_max() (in module pyrosetta.rosetta.protocols.frag_picker) sa_norm() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) safe() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) safe_read() (in module pyrosetta.rosetta.core.chemical.gasteiger) safe_secstruct() (in module pyrosetta.rosetta.protocols.jumping) safe_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) safe_set_extended_torsions_and_idealize_loops() (in module pyrosetta.rosetta.protocols.loops) safe_write() (in module pyrosetta.rosetta.core.chemical.gasteiger) safely_append_polymer_residue_after_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) safely_prepare_statement() (in module pyrosetta.rosetta.basic.database) safely_prepend_polymer_residue_before_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) safely_read_from_database() (in module pyrosetta.rosetta.basic.database) safely_write_to_database() (in module pyrosetta.rosetta.basic.database) SaltBridgeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) same() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) same_chain() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) same_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) same_ignoring_spaces() (in module pyrosetta.rosetta.utility) same_link() (in module pyrosetta.rosetta.core.io) same_pose() (in module pyrosetta.rosetta.protocols.denovo_design) same_type() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) same_type_as_me() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) SameSequenceAndDSPositionGrouper (class in pyrosetta.rosetta.protocols.match.output) SameSequenceGrouper (class in pyrosetta.rosetta.protocols.match.output) SameStrand (class in pyrosetta.rosetta.protocols.jumping) sample_all_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sample_all_conformers() (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) sample_all_rotations_at_jump() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) sample_beta() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sample_farnesyl() (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) sample_first() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_level() (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) sample_loops() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) sample_near_nucleoside_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) sample_near_suite_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) sample_ONLY_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sample_pH() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sample_proton_chi() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) sample_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) sample_second() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_strategy_for_chi() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) sample_third() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_types() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) sample_zero_probs_at() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) SampleFarnesylMover (class in pyrosetta.rosetta.protocols.farnesyl) sampler_assert_no_virt_sugar_sampling() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_extra_beta_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_extra_epsilon_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_include_torsion_value_in_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_max_centroid_distance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_num_pose_kept() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_perform_phosphate_pack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_silent_file() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) sampler_try_sugar_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) SamplerPlusPlusType (class in pyrosetta.rosetta.protocols.toolbox) samples() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) SampleStrategyData (class in pyrosetta.rosetta.protocols.match.upstream) SampleTiltAngles (class in pyrosetta.rosetta.protocols.membrane.benchmark) sampling_data() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) sampling_data_setup() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) sampling_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) SandwichFeaturesCreator (class in pyrosetta.rosetta.protocols.features.strand_assembly) SaneMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) SAnode (class in pyrosetta.rosetta.core.scoring.power_diagram) sasa() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) SasaCalc (class in pyrosetta.rosetta.core.scoring.sasa) sasaF2() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) SasaMethod (class in pyrosetta.rosetta.core.scoring.sasa) SasaMethodEnum (class in pyrosetta.rosetta.core.scoring.sasa) SasaMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SasaRadii (class in pyrosetta.rosetta.core.scoring.sasa) save_all_in_one() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) save_archive() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) save_binary() (pyrosetta.rosetta.protocols.cluster.APCluster method) save_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) save_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) save_cluster_tree() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) save_decoys() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) save_energy() (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) save_fragments() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) save_into_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) save_momento() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) save_schema() (in module pyrosetta.rosetta.protocols.rosetta_scripts) save_status() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) save_to_file() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) save_trial_number_to_checkpoint() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) SaveAndRetrieveSidechains (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) saved_accept_file_name() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) saved_reference_pose() (in module pyrosetta.rosetta.protocols.rosetta_scripts) saved_trial_number_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) SavePDBInfoMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) SavePoseConstraintToFileFilter (class in pyrosetta.rosetta.protocols.constraint_filters) SavePoseMover (class in pyrosetta.rosetta.protocols.rosetta_scripts) saveState() (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) sbisect() (in module pyrosetta.rosetta.numeric.kinematic_closure) sc_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) sc_only() (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) scaf_name() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) scalar() (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) scalar_weighted() (in module pyrosetta.rosetta.protocols.constraint_generator) ScalarOption (class in pyrosetta.rosetta.utility.options) ScalarOptionKey (class in pyrosetta.rosetta.utility.options) scale_axis_stagger() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) scale_factor() (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) scale_temperatures() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) ScaleMapIntensities (class in pyrosetta.rosetta.protocols.electron_density) scaling() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) SCAN (class in pyrosetta.rosetta.core.pack.task) SCdisplayState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) schema() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) score() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) score_basis() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) score_basis_125() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) score_by_scoretype() (pyrosetta.rosetta.core.scoring.ScoreFunction method) score_delta() (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) score_diff_after_minimization() (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) score_disulfide() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) score_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) score_filter() (pyrosetta.rosetta.core.io.silent.SilentFileData method) score_fragment() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) score_fragment_from_cache() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) score_function() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover 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.SaneMinMover 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.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) score_function_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) score_map() (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) score_one() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) score_only() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) score_pose() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) score_res_z() (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) score_table_filename() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_labels() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_lines() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_weights() (pyrosetta.rosetta.core.io.StructFileRep method) score_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) score_type() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint 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.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) score_type_2_active() (pyrosetta.rosetta.core.scoring.EnergyGraph method) score_type_from_name() (in module pyrosetta.rosetta.core.scoring) score_types() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) score_types_by_method_type() (pyrosetta.rosetta.core.scoring.ScoreFunction method) score_types_for_method() (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) score_variation() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) score_variations() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) score_zero_scores() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) scored_base_pair_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) scored_frag_close() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) scored_frag_cycle_ratio() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) ScoreEValuator (class in pyrosetta.rosetta.protocols.frag_picker.scores) ScoreEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) scorefile_name() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) ScoreFileSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) ScoreFunction (class in pyrosetta.rosetta.core.scoring) scorefunction() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) ScoreFunctionFactory (class in pyrosetta.rosetta.core.scoring) ScoreFunctionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ScoreFunctionInfo (class in pyrosetta.rosetta.core.scoring) ScoreFunctionLoader (class in pyrosetta.rosetta.protocols.parser) scorefxn() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) scorefxn_cen_cst() (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) scorefxn_low() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) scorefxn_minimize() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) scorefxn_pack() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) scorefxn_rama_cst() (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) scorefxn_repack() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) scorefxn_update_from_options() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) ScoreJumpFileSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) scoreline_prefix() (pyrosetta.rosetta.core.io.silent.SilentStruct method) ScoreOnlyJobOutputter (class in pyrosetta.rosetta.protocols.jd2) scores() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) scores_present() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) ScoreStructText (class in pyrosetta.rosetta.core.io.raw_data) ScoreType (class in pyrosetta.rosetta.core.scoring) ScoreTypeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) scoring() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) scoring_begin() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) scoring_end() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) scoring_grid_loader_ct_namer() (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) ScoringGridLoader (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) SCPA_cyclization_type (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) scratch_pose() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) screen_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) ScreeningFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SCS_Helper (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_MultiTemplate (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_Result (class in pyrosetta.rosetta.protocols.antibody.grafting) sd() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) sd_ang() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_dih() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_dis() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) sdev() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) sealed_symmetric_fold_tree() (in module pyrosetta.rosetta.core.pose.symmetry) SealFoldTreeMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) search_x() (in module pyrosetta.rosetta.core.scoring.packstat) secant() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) secant_interpolation() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) SecMatchEvaluatorFactory (class in pyrosetta.rosetta.protocols.match.downstream) SecMatchResiduePairEvaluator (class in pyrosetta.rosetta.protocols.match.downstream) secondary_shifts() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) secondary_structure_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) SecondaryIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SecondaryMatcherToDownstreamResidue (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryMatcherToUpstreamResidue (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryMatchUpstreamResProcessor (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryPoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) SecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SecondaryStructure (class in pyrosetta.rosetta.core.fragment) SecondaryStructureMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SecondaryStructureMPM (class in pyrosetta.rosetta.protocols.match) SecondaryStructurePool (class in pyrosetta.rosetta.protocols.frag_picker.quota) SecondaryStructurePotential (class in pyrosetta.rosetta.core.scoring) SecondaryStructureSegmentFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SecondaryStructureType (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) SecondaryStructureWeights (class in pyrosetta.rosetta.core.scoring) secstruct() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.frags.VallData method) SecStructGen (class in pyrosetta.rosetta.core.fragment.picking_old.vall.gen) SecStructMinimizeMultiFunc (class in pyrosetta.rosetta.protocols.ncbb) section() (in module pyrosetta.rosetta.protocols.sparta) section_index() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) see_edge_or_core_or_loop_or_short_edge() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_model_is_H_bonded_by_terminal_strands() (in module pyrosetta.rosetta.protocols.legacy_sewing) see_whether_sheet_is_antiparallel() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_sheets_can_be_combined() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_this_sw_has_SS_bond() (in module pyrosetta.rosetta.protocols.features.strand_assembly) seed() (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) seek_beg() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) seekp() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) Segment (class in pyrosetta.rosetta.protocols.denovo_design.components) segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) segment1_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) segment2_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) segment_ids() (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) segment_length() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) segment_to_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) segment_to_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) SegmentedAtomPairConstraintGenerator (class in pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator) SegmentGraph (class in pyrosetta.rosetta.protocols.legacy_sewing) segmentID() (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.pose.PDBInfo method) SegmentInsert (class in pyrosetta.rosetta.protocols.forge.build) SegmentRebuild (class in pyrosetta.rosetta.protocols.forge.build) segments() (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) SegmentSwap (class in pyrosetta.rosetta.protocols.forge.build) select() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) select_best_poses() (in module pyrosetta.rosetta.protocols.ligand_docking) select_cav_balls() (in module pyrosetta.rosetta.core.scoring.packstat) select_epitope_residues() (in module pyrosetta.rosetta.protocols.antibody) select_final_loop() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) select_fragments() (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) select_interface_residues() (in module pyrosetta.rosetta.protocols.interface) select_loop_frags() (in module pyrosetta.rosetta.protocols.loops) select_loop_residues() (in module pyrosetta.rosetta.protocols.loops) select_only_alpha_aas() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) select_only_FAMILYVW() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) select_orient_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) select_points() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) select_poses() (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) select_positive_phi() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) select_random() (pyrosetta.rosetta.protocols.jumping.JumpSelector method) select_RBsegments() (in module pyrosetta.rosetta.protocols.rbsegment_relax) select_score() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) selected() (pyrosetta.rosetta.protocols.moves.SwitchMover method) SelectedResidueCountMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResiduesMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResiduesPyMOLMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) selection_is_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) selection_positions() (in module pyrosetta.rosetta.core.select.residue_selector) selector() (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) Selector_AA (class in pyrosetta.rosetta.core.chemical) Selector_CMDFLAG (class in pyrosetta.rosetta.core.chemical) Selector_HAS_ATOMS (class in pyrosetta.rosetta.core.chemical) Selector_MATCH_VARIANTS (class in pyrosetta.rosetta.core.chemical) Selector_NAME1 (class in pyrosetta.rosetta.core.chemical) Selector_NAME3 (class in pyrosetta.rosetta.core.chemical) Selector_NO_VARIANTS (class in pyrosetta.rosetta.core.chemical) Selector_PROPERTY (class in pyrosetta.rosetta.core.chemical) selector_type (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector) Selector_UPPER_POSITION (class in pyrosetta.rosetta.core.chemical) Selector_VARIANT_TYPE (class in pyrosetta.rosetta.core.chemical) SelectorLogicParser (class in pyrosetta.rosetta.core.select.residue_selector) SelectResiduesWithinChainOperation (class in pyrosetta.rosetta.protocols.task_operations) send_char_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_data_to_head_node() (in module pyrosetta.rosetta.basic.mpi) send_double_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_doubles_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_integer_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_integers_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_size_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_sizes_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) send_string_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) sendMessage() (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) seq1() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) seq2() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) seq_design_strategy_to_enum() (in module pyrosetta.rosetta.protocols.antibody.design) seq_design_strategy_to_string() (in module pyrosetta.rosetta.protocols.antibody.design) SeqDesignStrategyEnum (class in pyrosetta.rosetta.protocols.antibody.design) seqmap() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) seqpos() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) seqpos_for_geomcst() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) seqposes_no_mutate_str() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) seqprof() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) seqprof_wt_aa() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) seqs_from_cmd_lines() (in module pyrosetta.rosetta.core.sequence) sequence() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) sequence_comment_id() (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) sequence_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) sequence_map_from_pdbinfo() (in module pyrosetta.rosetta.core.pose) sequence_mapping() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) sequence_matches() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) sequence_mutated() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) sequence_space() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) SequenceAlignmentHasher (class in pyrosetta.rosetta.core.sequence) SequenceCoupling1BDConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) SequenceCouplingConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) SequenceCreator (class in pyrosetta.rosetta.core.sequence) SequenceDistance (class in pyrosetta.rosetta.protocols.simple_filters) SequenceIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SequenceMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SequenceMotifTaskOperation (class in pyrosetta.rosetta.protocols.task_operations) SequenceMover (class in pyrosetta.rosetta.protocols.moves) SequenceProfileConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) SequenceShiftMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) sequential_order() (pyrosetta.rosetta.protocols.loops.Loops method) serialize() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) serialize_graph_json() (in module pyrosetta.rosetta.protocols.legacy_sewing) serialize_ids() (in module pyrosetta.rosetta.protocols.features) serialize_residue_xyz_coords() (in module pyrosetta.rosetta.protocols.features) serialize_weights() (pyrosetta.rosetta.core.scoring.ScoreFunction method) SerializedLoop (class in pyrosetta.rosetta.protocols.loops) Set() (in module pyrosetta) set() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) Set_AA (class in pyrosetta.rosetta.core.chemical) set_aa() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) set_aa_composition_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_aa_probabilities() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_aa_probabilities_from_file() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_aa_probability_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_ab_fold_tree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) set_ab_info() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) set_abba_bins_binfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_abego() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) set_abort_on_failed_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_absolute_stereochemistry() (pyrosetta.rosetta.core.chemical.Atom method) set_absolute_threshold() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) set_abstract() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) set_accept_aborted_loops_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_accept_blocks_missing_header() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_acceptor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_accessed() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) set_active_restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_active_site_grid() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_add_alanine_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_c_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_constraints() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_add_hydrophobic_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_lead_zero_to_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_add_ligand_to_pose() (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) set_add_n_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_overall_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_peptide_plane_variants() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_add_target_to_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) set_add_target_types() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_add_to_current() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_add_virt_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_add_virt_res_as_root() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_additional_task_operarations() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_additional_type_to_add() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_additional_type_to_remove() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_adduct_flag() (pyrosetta.rosetta.core.chemical.ResidueType method) set_aggregate_function() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) set_akash_dyepos() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_align_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_align_only_over_base_atoms() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_align_to_native() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_all_chi() (pyrosetta.rosetta.core.conformation.Residue method) set_all_current_jobs_as_deletable() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_all_extra_parameters() (pyrosetta.rosetta.core.chemical.AtomType method) set_all_nu() (pyrosetta.rosetta.core.conformation.Residue method) set_all_ring_nu() (pyrosetta.rosetta.core.conformation.Residue method) set_allow_anchor_repack() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_allow_base_pair_only_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_allow_bondangles() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_allow_bondlengths() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_allow_bulge_at_chainbreak() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_allow_chain_boundary_jump_partner_right_at_fixed_BP() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_allow_design_cdr() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_design_neighbor_antigen() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_design_neighbor_framework() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_dihedrals() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_allow_fixed_res_at_moving_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_allow_rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_allow_syn_pyrimidine() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_allow_virtual_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_allow_virtual_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_allowed_failure_before_extend() (pyrosetta.rosetta.protocols.LoopRebuild method) set_allowed_failure_before_stop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_allowed_residues_by_position() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_alpha() (pyrosetta.rosetta.core.pose.Pose method) set_already_completed_job_count() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_alternative_search_paths() (pyrosetta.rosetta.utility.io.izstream method) set_always_rotamer_one() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) set_ambiguous_hnq() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) set_anchor_noise_constraints_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_anchor_via_constraints() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_ang_D1D2D3() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_ang_U1D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_ang_U2D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_angle() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_angle1_func() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle2_func() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle_atom() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_angle_exponent() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_angle_length_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_angle_max() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) set_angle_range() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) set_angle_ranges() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_angle_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_angle_sd() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle_shift_factor() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_angle_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_angles() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) set_antibody_info() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) set_antiparallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_apply_vdw_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_apply_virtual_res_variant_at_dinucleotide() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_architect() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_archive() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) set_assert_jump_point_in_fixed_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_asymm_unit_fold_tree() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) set_atmid() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_atom_base() (pyrosetta.rosetta.core.chemical.ResidueType method) set_atom_level_domain_map() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_atom_mode() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_atom_names_for_distance_measure() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_atom_pair_func() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atom_pair_sd() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atom_type() (pyrosetta.rosetta.core.chemical.ResidueType method) set_atom_type_set() (pyrosetta.rosetta.core.chemical.ResidueType method) set_atoms1() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atoms2() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atoms_per_residue() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_atr_rep_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_atr_rep_screen_for_docking() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_attach_boinc_ghost_observer() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_attached_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) set_attachment_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) set_attachments() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_auto_detect_glycan_connections() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_auto_detect_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_auto_tune() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_auto_update() (pyrosetta.rosetta.core.scoring.NeighborList method) set_autofoldtree() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) set_autotemp() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_babmotifs() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) set_backbone() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_backbone_backbone_acceptor() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_backbone_backbone_donor() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_backbone_burial() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) set_backbone_exposed() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) set_backbone_heavyatom() (pyrosetta.rosetta.core.chemical.ResidueType method) set_backbone_only() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_bad() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) set_bad_nter() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) set_ball_radius() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_base_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_base_partner() (in module pyrosetta.rosetta.core.scoring.dna) set_base_segment_chainbreak_constraints() (in module pyrosetta.rosetta.protocols.dna) set_base_type_cop() (pyrosetta.rosetta.core.chemical.ResidueType method) set_bb() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_bb_bb() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_bb_grid() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_bb_movemap() (in module pyrosetta.rosetta.protocols.hydrate) set_bb_torsion() (in module pyrosetta.rosetta.core.pose) set_bb_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_behaviour() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_being_set() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_beta() (pyrosetta.rosetta.core.pose.Pose method) set_bfactors_from_atom_id_map() (in module pyrosetta.rosetta.core.pose) set_bias_sampling() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_bIdealLoopClosing() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) set_bin() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_bin_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_bin_params_file_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_binfile_and_load() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_bInitDofs() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_binname() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_blueprint() (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_boltz_rank() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_boltzmann_temp() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) set_bond_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) set_bond_length() (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) set_boolean_option() (in module pyrosetta.rosetta.basic.options) set_boolean_vector_option() (in module pyrosetta.rosetta.basic.options) set_bounded() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_bounded_width() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) set_bounding_box() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_bps_moves() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_branch_atom() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_branches() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_branches_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_bridge() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_bridge_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_broker() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_buffer_length() (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_build_all_loops_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_build_attempts_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_build_overlap() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_build_round1_hits_twice() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) set_bulge_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_bulges() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) set_bump_check() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_bump_overlap_factor() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_bump_tolerance() (pyrosetta.rosetta.protocols.match.Matcher method) set_bundle_symmetry() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_bundle_symmetry_copies() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_burial_cutoff() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_c_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_ca_only() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_cache_selection() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_cache_size() (in module pyrosetta.rosetta.basic.database) set_cacheable_cluster_data_to_pose() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) set_cached_resfile() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) set_calc_dSASA() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_calc_hbond_sasaE() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_calc_in_hours() (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) set_calc_rms_res() (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.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_calculate_jacobians() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_calculate_silent_Es() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_calculated() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) set_calculation_method() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_calculator_by_name() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) set_camelid() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) set_can_be_deleted() (pyrosetta.rosetta.protocols.jd2.Job method) set_candidates_collector() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_cart_min() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_cartesian() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_cartesian_bonded_linear() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_cartesian_bonded_parameters() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_cartesian_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_catalytic_atoms() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_ccd_close() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_ccd_close_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) set_CCD_torsions_to_zero() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) set_cdr() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) set_CDR_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) set_cdr_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_cdr_only() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_cdr_range() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_cdr_set_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_cen_scorefunction() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_cen_scorefxn() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) set_center() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) set_center_jumps_in_single_stranded() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_centroid() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) set_centroid_loop_building() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_centroid_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_centroid_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_centroid_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_chainbreak_max() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) set_chainbreak_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_chains() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_chains_whose_residues_are_separate_chemical_entities() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_change_chi_without_replacing_residue() (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) set_changed() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) set_check_if_residues_are_Ctermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_check_if_residues_are_Ntermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_check_ss() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_chemical_bond_from_upstream_to_downstream() (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_chi() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_chi_according_to_coordinates() (in module pyrosetta.rosetta.core.conformation) set_chi_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_choices() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) set_choose_random() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_cis_peptide_bonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_cl_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) set_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) set_cluster_by_all_atom_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_cluster_csts_data_cutoff() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_csts_use_mean_cst_data() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_csts_use_outlier_data() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_data() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) set_cluster_radius() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_cluster_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_clusters() (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) set_combine_long_loop_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_command() (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) set_comp_constraint_aa() (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) set_comparer_info() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) set_comparison_pose() (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) set_comparison_type() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_completed() (pyrosetta.rosetta.protocols.jd2.Job method) set_composite_action() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_compute_interface_delta_hbond_unsat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_interface_sc() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_packstat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_compute_separated_sasa() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_computed() (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) set_cone_parameters() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_conformer_sampling_sd() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_connect_info_cutoff() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_cons_design_data_source() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_conserved() (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) set_consider_mainchain_only() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) set_const_data() (pyrosetta.rosetta.core.pose.Pose method) set_constrain_to_closest() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_constraint_func() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) set_constraint_weight() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_constraints() (in module pyrosetta.rosetta.protocols.rbsegment_relax) set_constraints_from_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_constraints_only() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_contact_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_contact_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_coord_frame_ref() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) set_coordinate_cacher() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) set_coordinate_constraints_during_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_coordinates() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) set_copy_DOF() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_copy_identity() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_copy_torsions() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_corresponding_atoms_robust() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) set_cos_theta() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) set_count_gly_as_polar() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_crystinfo() (pyrosetta.rosetta.core.pose.PDBInfo method) set_cst_action() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_cst_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_cst_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_cst_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_cst_weight() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_cstAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) set_cstfile() (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) set_cstio() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_cstweight() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_current_confnum() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) set_current_job() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.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.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover 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.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover 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.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_current_tag() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.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.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover 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.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover 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.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_custom_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_custom_dihedral() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) set_custom_rama_table() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_cut() (pyrosetta.rosetta.protocols.loops.Loop method) set_cutoff() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_cutoff_buried_surface_area() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_cutoff_distance() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_cutoffs() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_cutpoint_closed_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_cycles_inner() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) set_cycles_outer() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) set_cyclization_type() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_d() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_D_alpha_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_D_beta_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_data_source() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) set_database_name() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) set_database_pq_schema() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) set_db_path() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_db_reporter() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_dcut() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) set_dcut1() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) set_dcut2() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) set_ddG_cutoff() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) set_debug() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) set_decoy_compatibility() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_decoy_tag() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_decoys_returned() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_deep_optimization() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) set_default() (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 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.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_default_coordinate_settings() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_final_stream() (pyrosetta.rosetta.basic.TracerImpl method) set_default_mc() (pyrosetta.rosetta.protocols.LoopRebuild method) set_default_minimization_settings() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_minimizer() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_movemap() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_moveset_phase1() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_moveset_phase2() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_moveset_phase3() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_options() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_default_scores() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_default_settings() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_default_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_defaults() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions 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.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_degree_vicinity() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_degrees() (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) set_delta() (pyrosetta.rosetta.core.pose.Pose method) set_delta_omega0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_delta_omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_delta_omega1_all() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_delta_t() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_delta_z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_density_sc_scale_byres() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_deriv_check_result() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) set_deriv_cutoff() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) set_design() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_design_framework_conservative() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_framework_conserved_res() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_H3_stem() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_loop() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_design_neighbors() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_design_options() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_design_protocol() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_design_target_res() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) set_design_taskset() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_design_x_positions() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_designing_with_noncanonicals() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_desymmeterize() (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) set_detect_bonds() (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_detect_pseudobonds() (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_dew_waters_not_to_be_included() (in module pyrosetta.rosetta.protocols.hydrate) set_dG_weight() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_dihedral() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_dihedral_constraint_weight() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_dihedral_mask() (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_dihedrals_from_linkage_conformer_data() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_dimension() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) set_dis() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_dis_D1D2() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_dis_D2D3() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_disable_packing_and_design() (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) set_disable_sampling_of_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_disabled_except_during_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) set_disallow_deletion_of_last_residue() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_disallow_pack_polar_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_disallow_realign() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_dist_cutoff_multiplier() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_dist_exponent() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_distance() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) set_distinguish_pucker() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_disulfide_atom_name() (pyrosetta.rosetta.core.chemical.ResidueType method) set_disulfide_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_do_add_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_do_inner() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_do_not_autoassign_SS() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_do_not_sample_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_do_outer() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_do_sfxn_eval_every_iteration() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_dock_each_chunk() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_dock_each_chunk_per_chain() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_dock_high_res_scorefunction() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_dock_low_res_scorefunction() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_dock_mcm_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_dock_min() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_dock_min_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_dock_pert() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_dock_post_graft() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_dock_ppk() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_dock_ppk_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_dock_rounds() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_dock_rtmin() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_docking_highres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_docking_local_refine() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_dof() (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.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pose.Pose method) set_DOF() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) set_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_donor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_donor_structure() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_downstream_algorithm() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_downstream_builder() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_downstream_master() (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) set_downstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_downstream_restype() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_drift() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_dry_run() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_dSASA_cutoff() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_dsbuilder() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_dump() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_dump_pdb() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_dump_silent() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_dumping_app() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_edge_data() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) set_edge_weight() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_effective_sequence_separation() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) set_efficiency() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_elec_sigmoidal_die_params() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_else() (pyrosetta.rosetta.protocols.filters.IfThenFilter method) set_end() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) set_end_bias() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_energy() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) set_energy_cutoff() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_energy_landscape_evaluator() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) set_energy_method_options() (pyrosetta.rosetta.core.scoring.ScoreFunction method) set_ensemble1() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_ensemble2() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_ensured_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_entity_element() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) set_entity_template() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) set_enumerate() (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) set_enumeration_shell() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) set_enzio_param() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_enzyme() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_epitope_residues() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_epsilon() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_equiv() (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) set_error_on_out_of_bounds_index() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) set_errorfull_deltaE_threshold() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_etable() (pyrosetta.rosetta.core.scoring.ScoreFunction method) set_euler_bin_widths() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_evaluate_local() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) set_evaluation() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) set_evaluators() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) set_exclude_chain_termini() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_exclude_polar_atoms_by_charge() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_excluded_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_exit_if_missing_heavy_atoms() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_expand_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_explicit_hydrogen_included_radii_set() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_expression() (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) set_extend_h3() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) set_extend_ss() (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) set_extended() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) set_extended_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_extended_torsions() (in module pyrosetta.rosetta.protocols.loops) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_extended_torsions_and_idealize_loops() (in module pyrosetta.rosetta.protocols.loops) set_external_position() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_external_position_for_resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_external_position_for_resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_extra_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_extra_data_1() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_extra_data_2() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_extra_data_3() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_extra_minimize_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_extra_parameter() (pyrosetta.rosetta.core.chemical.AtomType method) set_extra_penalty() (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) set_extra_samples() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) set_fa_dun_cutoff() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_fa_dun_cutoff_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_fa_score_function() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_fa_scorefunction() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_fa_scorefxn() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) set_fallback_strategy() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_farray_from_sso() (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) set_favor_native_bonus() (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) set_fcen10() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_fcen12() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_fcen6() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) set_file_option() (in module pyrosetta.rosetta.basic.options) set_file_reading_token() (pyrosetta.rosetta.protocols.loops.Loops method) set_file_vector_option() (in module pyrosetta.rosetta.basic.options) set_filename() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) set_filter() (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) set_filter_behaviour() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_filter_by_lj() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_filter_by_phipsi() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_filter_during_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_filter_native_big_bins() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_filter_out_high() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_filter_out_low() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_filter_structs() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_filter_type() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_filter_user_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_filter_virtual_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_filters() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_final_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_final_min_pack_min() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_finer_sampling_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_finish_scorefxn() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_finite() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) set_first_expression() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) set_fitness() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) set_fix_angles() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fix_backbone() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_fix_catalytic_aa() (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) set_fix_lengths() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fix_torsions() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fixed_energies() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) set_fixed_if_moving() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_fixed_res() (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.StepWiseWorkingParametersSetup method) set_fixed_residues() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_flank_size() (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) set_floating_base() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_floating_base_anchor_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_focus() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_focus_selector() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_focused_geomcst_id() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_fold_tree_from_symm_data() (in module pyrosetta.rosetta.core.conformation.symmetry) set_fold_tree_io() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_fold_tree_root() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) set_folder() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_folding_window() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) set_foldtree() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) set_force_align() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_force_anti_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_bitflip() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_force_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_force_cluster() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_force_internal() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_job_purging() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_force_north_paper_db() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_force_north_sugar_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_phosphate_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) set_force_repack() (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) set_force_south_sugar_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_syn_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_user_defined_jumps() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_forced_silent_struct_type() (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_fraction() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) set_fractions() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) set_frag3() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_frag_files() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_frag_size() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) set_frag_sizes() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_fragments() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_free_peptide() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) set_free_rsd() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_from_cdr() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) set_from_other_chains() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_from_same_chain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_from_scheme() (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) set_ft_mover() (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) set_full_length_loop_rmsd_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) set_full_model_parameters() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_full_repack() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_full_to_sub() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_fullatom() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_fullatom_loop_building() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_fullatom_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_fullatom_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_function() (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) set_Fv() (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) set_gamma() (pyrosetta.rosetta.core.pose.Pose method) set_gasteiger_atom_type() (pyrosetta.rosetta.core.chemical.ResidueType method) set_gasteiger_typeset() (pyrosetta.rosetta.core.chemical.ResidueType method) set_gaussian() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) set_gaussian_stdevs_recces_turner() (in module pyrosetta.rosetta.protocols.recces) set_gaussian_stdevs_thermal_sampler() (in module pyrosetta.rosetta.protocols.recces) set_general_phi_sd() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_general_psi_sd() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_generous_hbonds_() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_geomcst_for_superposition_from_enz_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) set_ghost_loops() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_global() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) set_global_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_global_sample_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_glycam_pdb_format() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_glycan_iupac_bb_torsions() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycan_iupac_chi_torsions() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycan_relax_rounds() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_glycan_sequon_type() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_GlyCorrection_values_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_glycosidic_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycosylation() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_glycosylation_position() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_glycosylation_weights() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_glycosylations() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_graft_design_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_graft_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_grow_attempts_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_guarantee_no_DNA() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_guarded_loops_not_in_charge() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_handedness_score_flag() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_hardsphere_bump_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_has_silent_in() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_hash_euclidean_bin_width() (pyrosetta.rosetta.protocols.match.Matcher method) set_hash_euclidean_bin_widths() (pyrosetta.rosetta.protocols.match.Matcher method) set_hash_euler_bin_width() (pyrosetta.rosetta.protocols.match.Matcher method) set_hash_euler_bin_widths() (pyrosetta.rosetta.protocols.match.Matcher method) set_hb_e_cutoff() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_hbnet_energy_ramping() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) set_hbond_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) set_hbond_options() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_hbonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_heat_after_cycles() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_helix() (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) set_helix_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_helix_to_copy() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_highres_score_func() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_highres_scorefxn() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_hit_cacher() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) set_hydrate_magnesiums() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_icoor() (pyrosetta.rosetta.core.chemical.ResidueType method) set_id() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect 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.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_ideal_abego() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_ideal_angle_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_angle_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_3() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_distance() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_xyz() (pyrosetta.rosetta.core.chemical.ResidueType method) set_idealize() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_idealize_h3_stems() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) set_idealize_insert() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_idealize_loop_first() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_idealize_torsions() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_IGEdgeReweights() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) set_ignore_bb_heavy_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_ignore_default_docking_task() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_ignore_default_task() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_ignore_FARFAR_no_auto_bulge_parent_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_FARFAR_no_auto_bulge_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_light_chain() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_ignore_pose_datacache() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_ignore_pose_profile_length_mismatch() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) set_ignore_segments() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) set_ignore_sugars() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_ignore_surface_res() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_ignore_unconnected_upper() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) set_ignore_unmatched_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_ignore_waters() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_ignore_zero_occupancy() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_implicit_hydrogen_included_radii_set() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_carbon_sulfer_only_in_hydrophobic_calc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_cdr4_in_optimization() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_include_default_linear_chainbreak() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_include_focus_in_subset() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_include_hydrogens_explicitly() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_native_restype() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_include_native_type() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_include_neighbors() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_include_probe_radius_in_atom_radii() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_probe_radius_in_calc() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_include_protein_omega() (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) set_include_root() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_indent() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) set_index() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) set_inherit_scorefxn_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_inner_ca_only() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_inner_min_seq_sep() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_sd() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_unweighted_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_use_harmonic_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_weight() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_input_pose() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.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.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover 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.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover 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.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_input_set() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) set_input_set_selector() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_input_tags() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_insert_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_insert_region() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) set_instruction_file() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_instruction_file_path() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) set_integer_option() (in module pyrosetta.rosetta.basic.options) set_integer_vector_option() (in module pyrosetta.rosetta.basic.options) set_integration_test_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_intensity() (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) set_interface() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_interface_chains() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_interface_definition_task_operation() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_interface_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_interface_distance() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) set_interface_jump() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_intermediate_structs() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_internal_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_interval() (pyrosetta.rosetta.protocols.checkpoint.Timer method) set_invert() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_invert_helix() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_invert_task() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) set_invrots_for_listnum() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) set_ios_hook() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) set_is_do_minimize() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_cyclic_poses() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_peptide_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_prepared_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_report_file() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_report_gzip() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_skip_zero_isc() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_iterations() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) set_iterations_per_phase() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_job_inputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobsContainer 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) set_job_outputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) set_jobindex_on_originating_node() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_jump() (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.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) set_jump_atom_stub_id() (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) set_jump_atoms() (pyrosetta.rosetta.core.kinematics.FoldTree method) set_jump_now() (pyrosetta.rosetta.core.kinematics.AtomTree method) set_jump_num() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_jump_point_pair_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_jump_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_jump_sample() (pyrosetta.rosetta.protocols.jumping.JumpSetup method) set_jump_selector() (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) set_jumpAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) set_just_polar_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_just_rna_backbone() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_keep_covalent() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_keep_filters() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_keep_input_foldtree() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_keep_input_protonation_state() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_keep_pdb_info_labels() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_keep_pose_in_memory() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_keep_task_allowed_aas() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_keep_top_designs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_keep_unknown_aas() (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) set_keep_virtual_residues() (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) set_kic_modeler_if_relevant() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_kic_sampling() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_kinematics() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_kinmover() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_kt() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_kT() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_L_alpha_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_L_beta_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_label() (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_landing_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_landing_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_last_accepted() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_last_accepted_pose() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_last_score() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_layer() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_as_greater_than_or_equal_to() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_as_less_than_or_equal_to() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_mode() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_layer_size() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_layers() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_length() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) set_lengths() (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) set_ligand_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ligand_jump_id() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligand_resnum() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligand_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ligand_weight() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligpose_rotamer() (in module pyrosetta.rosetta.protocols.match) set_limit() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_limit_only_to_length() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) set_linecount_offset() (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) set_linker_name() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_live() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) set_lj_atr_weight() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_cutoff() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_ramp_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_lj_ramp_inner_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_lj_rep_weight() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_sol_weight() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_local_movemap() (in module pyrosetta.rosetta.protocols.vip) set_local_refine() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_local_rotamer_id() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) set_localstrandpair_penalty() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_location_in_parent_node() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) set_logging_sink() (in module pyrosetta.logging_support) set_long_range_container() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_loop() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (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) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) set_loop_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loop_begin_and_end() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_loop_cluster_radius() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_loop_combine_rate_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_loop_cutpoint_in_pose_fold_tree() (in module pyrosetta.rosetta.protocols.loops) set_loop_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loop_file_name_and_reset() (pyrosetta.rosetta.protocols.loops.Loops method) set_loop_pose() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) set_loopres_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loopres_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loops() (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) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_loops_and_anchor() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_loops_from_file() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_loops_pointer() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) set_lores() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_low_energy_ring_conformers() (pyrosetta.rosetta.core.chemical.ResidueType method) set_low_res_protocol_only() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_lower_connect_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) set_lower_residues() (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) set_lower_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_lower_threshold() (pyrosetta.rosetta.protocols.filters.IfThenFilter method) set_lower_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_lowest() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_lowest_energy_ring_conformer() (pyrosetta.rosetta.core.chemical.ResidueType method) set_lowest_score_pose() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_lowres_score_func() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_lowres_scorefxn() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_lt_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_magnitude() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) set_mainchain_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) set_maintain_links() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_manager() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) set_mapfile_activated() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_match_string() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_max_accepted_trials() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_max_allowed_oversaturated() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_max_angle_disp_4() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_angle_disp_7() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_angle_disp_slope() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_attempts() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) set_max_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_max_decoys() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_max_distance() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) set_max_dslf_energy() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_max_dslf_pot() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_max_nstruct() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_radius() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_repeats() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_max_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_sample_iterations() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_max_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_max_struct() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_struct_per_radius() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_trial_num() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) set_max_tries_multiplier_for_ccd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_maxfrac() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) set_maxtrials() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_mc() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_mcfi() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_membrane() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_membrane_info() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) set_membrane_jump() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) set_memory_max_for_rpes() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_merge_behavior_manager() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) set_metal_bond_angle_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_bond_dist_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_bond_LJ_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metal_selector() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metals_angle_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metals_detection_LJ_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metals_distance_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_method_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) set_metropolis_hastings_mover() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) set_mg_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) set_min_allowed_score() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) set_min_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_min_bb() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_min_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_min_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_min_chi() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_min_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) set_min_frag_length() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_min_helix_length() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_min_num_south_sugar_filter() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_min_options() (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) set_min_overlap() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_min_rings() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_min_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_min_seq_sep() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_min_tol() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_min_tolerance() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_min_type() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minfrac() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) set_minimization_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_minimize_after_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) set_minimize_all() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_minimize_and_score_native_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minimize_and_score_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minimize_single_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_minimize_waters() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minimizer_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minimizer_rename_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_minmover() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_mintype() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_mirror_symm() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) set_mirrored_relative_to_type() (pyrosetta.rosetta.core.conformation.Residue method) set_missing_dens_as_jump() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_mm() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_mm_atom_type() (pyrosetta.rosetta.core.chemical.ResidueType method) set_mode() (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) set_model_and_remove_capping_residues() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_model_group() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) set_model_with_density() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_modes() (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) set_moltenres() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) set_monte_carlo() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) set_motif() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) set_motifs() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_movable_jumps() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) set_move_element() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_move_jumps_between_chains() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_move_map() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_move_map_for_centroid_loop() (in module pyrosetta.rosetta.protocols.loops) set_move_takeoff_torsions() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_move_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_moveable_jumps() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) set_movemap() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_movemap_factory() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_movemaps() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_movement() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) set_mover() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_mover_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_mover_tag() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_mover_weight() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_moves() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_moving_residues() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_mpi_rank() (pyrosetta.rosetta.utility.SimulateMPI method) set_mu() (pyrosetta.rosetta.core.pose.Pose method) set_multi_template_regions() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) set_multifunc() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) set_must_switch_bins() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_mut_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_mutate_to_glycine() (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) set_mutation_rate() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) set_my_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_n_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_n_cycle() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_n_cycles() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_n_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_n_frags() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_n_geometric_constraints() (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) set_n_helices() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_n_partners() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_n_sample() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_n_samples_per_side_of_nrchi_bin() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_n_samples_wi_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_name() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) set_name1() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) set_natbias_helices_sheet_pot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_natbias_hpairpot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_natbias_spairpot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_native() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_native_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_native_cdr_sequence() (in module pyrosetta.rosetta.protocols.antibody.design) set_native_distance_viol() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_native_edensity_score_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_native_in_mover() (in module pyrosetta.rosetta.protocols.jd2) set_native_pose() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.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.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover 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.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover 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.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_native_sequence() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) set_native_spairset() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) set_native_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_nbrs() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_ncluster() (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) set_ncycle() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_ncycles() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_neighbor_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_neighbor_distance() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_neighborhood_parameters() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) set_netcharge_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_network_anchoring() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_network_anchoring_per_residue() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_network_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_new_chain_order() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_new_conformation() (pyrosetta.rosetta.core.pose.Pose method) set_new_energies_object() (pyrosetta.rosetta.core.pose.Pose method) set_new_final_stream() (pyrosetta.rosetta.basic.TracerImpl method) set_new_fold_tree_initializer() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_next_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_next_correspondence() (pyrosetta.rosetta.utility.subset_mapping method) set_next_segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_nfrags() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) set_nhits_per_match() (pyrosetta.rosetta.protocols.match.HitHasher method) set_niter() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) set_no_chainend_ter() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_design_cys() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) set_no_detect_pseudobonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_filters() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_no_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_no_optH() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_output_cen() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_stem_copy() (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) set_noncanonical_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) set_nonideal() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_nonpivot_bb_torsion_id() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_nonpivot_res_to_sweep() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_nonpivot_torsion_sampling() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_normal() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) set_normalization_function() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) set_normalize_to_thk() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_nrchi_prob_minimum_for_extra_samples() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_nread_limit_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) set_nrepeat() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_nseq() (pyrosetta.rosetta.core.scoring.TMscoreStore method) set_nsteps() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_nstruct() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) set_nstruct_centroid() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_ntrial() (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) set_ntrials() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_nu() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_nu_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_nucleotide_to_A_form() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) set_num_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_num_geometric_constraints() (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_num_neighbors_counting_self_static() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) set_num_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) set_num_packs() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) set_num_pose_minimize() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_num_random_samples() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_num_states_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_num_trials() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) set_number_of_energy_sum_vertex_groups() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_nus() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_o2prime_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_obey_ENDMDL() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_occupied_space_bounding_box() (pyrosetta.rosetta.protocols.match.Matcher method) set_offset() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) set_omega() (pyrosetta.rosetta.core.pose.Pose method) set_omega0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_omega0_copies_pitch_instead() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_one_body_energy_for_node_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_only_stage4() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_open_mode() (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) set_optimize_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_optimize_cyclic_threshold() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_optimize_memory_usage() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_options() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_orbital_icoor_id() (pyrosetta.rosetta.core.chemical.ResidueType method) set_orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) set_original_pose() (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) set_original_scaffold_build_points() (pyrosetta.rosetta.protocols.match.Matcher method) set_original_scaffold_build_points_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_originating_node_MPI_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_out() (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) set_outer_ca_only() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_outer_max_distance() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_sd() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_unweighted_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_use_harmonic_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_weight() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outlier_use() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) set_output() (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) set_output_alternate_atomids() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_cluster_size() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_output_extra_RMSDs() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_output_file_name() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) set_output_filename() (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) set_output_in_rosetta_num() (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) set_output_min_pose() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_output_minimized_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) set_output_pdb() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_output_period() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_output_pose_cache_data() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_pose_energies_table() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_res_and_chain() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.core.pose.rna) set_output_secondary_structure() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_torsions() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_virtual() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_output_virtual_zero_occ() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_overall_aa_probabilities() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_overhang() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_overlap() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_owner() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_pack_all_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_pack_distance() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_pack_input() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_pack_interface_separated() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_pack_missing_sidechains() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_pack_neighbors() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_pack_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_pack_protein_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_pack_rounds() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_pack_separated() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_pack_shell() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) set_pack_together() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_pack_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_packer() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) set_packertask() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_parallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_param_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) set_param_from_options() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_param_index() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_parameter() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.MMAtomType method) set_paratope_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_parent() (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) set_parin_favorite_output() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_partner() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) set_partners() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_path_option() (in module pyrosetta.rosetta.basic.options) set_path_vector_option() (in module pyrosetta.rosetta.basic.options) set_PBP_clustering_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_pdb_comments() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_pdb_parents() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_penalty() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) set_pep_lengths() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_peptide_chain() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_per_chain_renumbering() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_perform_filters() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_perform_minimizer_run() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_perform_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_perform_VDW_rep_screen() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_perturb_CCD_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_KIC_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_show() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_temp() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_type() (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) set_perturbable() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_perturbation_magnitude() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_perturbation_type() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_perturber() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_perturber_effect() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_phi() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) set_phosphate() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_phosphate_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_picked_positions() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_picking_rounds() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_piece() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) set_pivot_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_pivot_picker() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) set_pivot_residue_selector() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_pivot_residues() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_pivots() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_placeholder() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) set_polar_charge_cutoff() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_polymeric_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) set_pool_name() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) set_population_based_conformer_sampling() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_pos() (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) set_pos_in_owners_list() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) set_pos_list() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) set_pose() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_pose_after_closure() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_pose_and_scorefxn_for_edens_scoring() (in module pyrosetta.rosetta.protocols.electron_density) set_pose_energy() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_pose_from_broker() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_pose_no_initialize() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) set_pose_reactive_sites() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_pose_start() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method)

set_poses() (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) set_position() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_positions_as_start_of_sequon() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_preapply() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_precision() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) set_prefix() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) set_prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_presample_added_residue() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_presample_by_swa() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_preserve_atom_coords() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_preserve_crystinfo() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_preserve_datacache() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_preserve_detailed_balance() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) set_preserve_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_preserve_whole_input_tag() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) set_primary_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_primary_strategy() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_print_out_info_to_pdb() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_prob() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_prob_random_pert_current() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_prob_sd_sampling() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_prob_uniform() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_prob_withinrot() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_probability_data_cutoff() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_probe_radius() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_proc_id() (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) set_ProCorrection_values_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_properties() (pyrosetta.rosetta.core.chemical.ResidueType method) set_property() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) set_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_protocol_and_batch_id() (in module pyrosetta.rosetta.protocols.features) set_protocol_info() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) set_proton() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) set_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) set_protonated_H1_adenosine_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_pseudobonds_to_residue() (pyrosetta.rosetta.core.conformation.Residue method) set_psi() (pyrosetta.rosetta.core.pose.Pose method) set_PyExitCallBack() (pyrosetta.rosetta.utility.py.PyExitCallback method) set_qsar_map() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) set_quench_mode() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_query_phi() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_phi_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_profile() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_psi() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_psi_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_sa() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_seq() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_quick_alignment() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_quota_score() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) set_r0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_r1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_r_array() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) set_r_inv_array() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) set_radial_disp_ranges() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_radial_disps() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_radii_set() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_rama_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_rama_cutoff_energy() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_rama_prepro_mainchain_torsion_potential_name() (pyrosetta.rosetta.core.chemical.ResidueType method) set_rama_prepro_map_file_name() (pyrosetta.rosetta.core.chemical.ResidueType method) set_rama_prepro_multiplier() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) set_rama_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_ramp_rama() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_ramp_vdw() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_random() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_random_confomer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) set_random_loop_flag() (pyrosetta.rosetta.protocols.LoopRebuild method) set_random_membrane_flip_angle() (pyrosetta.rosetta.protocols.membrane.FlipMover method) set_random_membrane_tilt_angle() (pyrosetta.rosetta.protocols.membrane.TiltMover method) set_random_order_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_randomize1() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_randomize2() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_randomize_missing_coords() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_randomize_resnum() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_range() (pyrosetta.rosetta.protocols.membrane.FlipMover method) set_ranges_unmodifiable() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_rank_score() (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) set_rb_center() (pyrosetta.rosetta.core.kinematics.Jump method) set_rb_constraints() (in module pyrosetta.rosetta.protocols.rbsegment_relax) set_rb_delta() (pyrosetta.rosetta.core.kinematics.Jump method) set_rb_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) set_read_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_read_only_ATOM_entries() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_read_pdb_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_real_option() (in module pyrosetta.rosetta.basic.options) set_real_vector_option() (in module pyrosetta.rosetta.basic.options) set_reasonable_fold_tree() (in module pyrosetta.rosetta.core.pose) set_rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_recces_turner_mode() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_reconstruct() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) set_record_source() (pyrosetta.rosetta.core.io.silent.SilentFileData method) set_recover_low() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) set_recover_sidechains_filename() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_recovery_threshold() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) set_recursion_limit() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) set_reference_energy() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) set_reference_pose() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_reference_pose_name() (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) set_refinable_lattice() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_refine() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_refine_pose_list() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) set_region() (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) set_reinitialize_CCD_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_relaxtype() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_relevant_atom_ids() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) set_relevant_residues_mode() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_remember_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_remember_unrecognized_water() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_remove_any_set_forced_cluster() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_remove_cterminus_variant() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_remove_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_remove_nterminus_variant() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_remove_target_types() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_rename_tags() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_renumber_pdb() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_repack() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_repack_list() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) set_repack_period() (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) set_repack_separated() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_repeat_tail_length() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_repeating_unit_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_repeats() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_report_all_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_all_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_as() (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) set_report_bb_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_crd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) set_report_format() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_report_nonheavy_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_sc_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_reporting() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_repulsive_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_require_mm_bend() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_required_connections_for_residue() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) set_res1() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_res2() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_res_name() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_res_type_set() (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) set_rescoords() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_rescore_only() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) set_reset_mode() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_resfile() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_resfile_1() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_resfile_2() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_resid() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) set_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_residue_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_residue_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_residue_mapping() (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) set_residue_name3() (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) set_residue_names() (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) set_residue_numbers() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_residue_pair_xform() (in module pyrosetta.rosetta.core.scoring.motif) set_residue_range() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_residue_range_not_surface() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_residue_sampling_from_pose_and_movemap() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_residue_selector() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) set_residue_selector1() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_residue_selector2() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_residue_selector_reference() (pyrosetta.rosetta.protocols.analysis.simple_metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) set_residue_subset() (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) set_residue_surface_cutoff() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_residue_type() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_residue_type_set_mode() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_residues() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) set_residues_for_atom_name_remapping() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_residues_per_repeat() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_resinfo() (pyrosetta.rosetta.core.pose.PDBInfo method) set_resnum() (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_resnum_string() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_restrict_only_design_to_loops() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_restrict_partners_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_restrict_receptors_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_restrictions_aa() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restrictions_append() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restrictions_exclude() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restype() (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) set_restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) set_rigid_body_confs() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) set_rigid_body_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ring_conformation() (pyrosetta.rosetta.core.pose.Pose method) set_rm_virt_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_rms_group_cutoff() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) set_rmsd() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) set_rmsd_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_rmsd_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_rmsd_type() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RMSDMetric method) set_rna_legacy_output_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_rna_secstruct_legacy() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) set_root() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) set_root_at_first_rigid_body() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_root_atom() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_roots() (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) set_rot_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_rotamer_operation() (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) set_rotamer_sampling_data_for_RLT() (in module pyrosetta.rosetta.core.pack.task.operation) set_rotamer_set_operation() (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) set_rotation() (pyrosetta.rosetta.core.kinematics.Jump method) set_rotation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_rotation_range() (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) set_rotation_std_dev() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_rottrial() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_rounds() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_rsd_set() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_rsd_type_name3() (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) set_rsd_type_set() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_rt_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_run_relax() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) set_run_snugdock() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) set_rv_infos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) set_safe() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_sample_all_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sample_beta() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sample_both_sugar_base_rotamer() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_sample_cis_pro_frequency() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_sample_index() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) set_sample_level() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_sample_nonpivot_torsions() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_sample_ONLY_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sample_pH() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_sample_range_large() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_sample_range_small() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_sample_startegy_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_sample_strategy_for_chi() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_sample_type() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_sample_zero_probs_at() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_sampler() (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_sampler_assert_no_virt_sugar_sampling() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_extra_beta_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_extra_epsilon_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_gaussian_stdev() (in module pyrosetta.rosetta.protocols.recces) set_sampler_include_torsion_value_in_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_max_centroid_distance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_num_pose_kept() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_perform_phosphate_pack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_silent_file() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_sampler_try_sugar_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_samples() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_sampletype() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_sampling_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_sasa_cutoff() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) set_sc_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_sc_neighbor_denominator() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_sc_neighbor_dist_midpoint() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_scaffold_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_scheme_conversion() (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) set_score() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge method) set_score_against_internal_contacts() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_score_component() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) set_score_cutoff() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) set_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_score_filter() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_score_function() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder 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.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) set_score_fxn() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_score_margin() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) set_score_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) set_score_type() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_score_weight() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_scorefunction() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.TotalEnergyMetric method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_scorefunction_min() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_scorefxn() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_scorefxn_deriver() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_scorefxn_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_scorefxn_low() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_scorefxn_min() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) set_scorefxn_minimize() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) set_scorefxn_pack() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) set_scorefxn_relax() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_scorefxn_repack() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) set_scoretype() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_scoretypes() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) set_sd() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_sd_ang() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_degree() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) set_sd_dih() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_dis() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_seal_foldtree() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_search_paths() (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) set_second_expression() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) set_secondary_residue_selector() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_secstruct() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_secstruct_from_bp() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) set_secstruct_from_dssp() (in module pyrosetta.rosetta.protocols.loops) set_secstruct_from_psipred_ss2() (in module pyrosetta.rosetta.protocols.loops) set_seed() (pyrosetta.rosetta.numeric.random.RandomGenerator method) set_segdef() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) set_segment() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) set_segment1_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_segment2_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_segment_IDs() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_select_designable() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_fixed() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_from_branch_residue() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_select_from_branch_residues() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_select_in_membrane() (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) set_select_only_alpha_aas() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_select_only_FAMILYVW() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_select_packable() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_positive_phi() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) set_selector() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_selector_type() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) set_separate_prt_ligand() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_seq_design_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_seq_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_seq_sep_scale() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_seqmap() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) set_seqprof() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) set_sequence() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_set_up_metal_bonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_sfxn() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_sfxn_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_shadowing_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) set_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) set_sheet() (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) set_sheet_topology() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) set_sheetlist() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_sheetlist_as_is() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_short_backrub_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_show_accessed_options_flag() (pyrosetta.rosetta.utility.options.OptionCollection method) set_show_all_fixes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_show_unused_options_flag() (pyrosetta.rosetta.utility.options.OptionCollection method) set_show_viol_level() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_sidechain() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_sidechain_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_silent_file() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_silent_file_data() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_silent_file_name() (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_silent_files_in() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_silentout_file_name() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_sim() (pyrosetta.rosetta.protocols.cluster.APCluster method) set_simple_append_map() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_simple_metric() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_simple_metrics() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) set_single_loop_fold_tree() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) set_single_resnum() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_size_and_nbb() (pyrosetta.rosetta.protocols.frags.TorsionFragment method) set_skip_chi_min() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_skip_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_skip_complicated_stuff() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_skip_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_skip_coord_constraints() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_skip_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_skip_reporting() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_skip_sampling() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_skip_set_reasonable_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_skip_stage1() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_skip_stage2() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) set_slice_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_solution_picker() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) set_sorter() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) set_source_size() (pyrosetta.rosetta.utility.subset_mapping method) set_span() (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) set_sparse_aa_info_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_special_edges() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) set_species() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) set_spin() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_ss() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_ss_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_ss_from_phipsi() (in module pyrosetta.rosetta.core.pose) set_ss_from_str() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) set_ss_lowstrand() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_ssid() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) set_SSorient() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) set_stage2_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage2_repack_period() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage3_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage4_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_start() (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) set_start_added_residue_in_aform() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_start_rep_weight() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_start_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_start_segments() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_starting_reference_energies() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) set_starting_rep() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) set_state_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_stats_cutoff() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_status() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) set_status_prefix() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) set_status_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) set_stem_size() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_step_size() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_stepwise_modeler() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) set_stop() (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.loops.Loop method) set_stop_after_closure() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_stop_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_stop_sampling() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_stop_segments() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) set_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_strand_extensions() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) set_strand_strand_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_strategy() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_stretch_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_strict_looprelax_checks() (pyrosetta.rosetta.protocols.loops.Loops method) set_strict_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) set_stride() (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) set_string_option() (in module pyrosetta.rosetta.basic.options) set_string_vector_option() (in module pyrosetta.rosetta.basic.options) set_strip_existing_glycans() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_struct_ids_from_sql() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) set_struct_ids_from_strings() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) set_stub_transform() (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) set_subelements_pick_one() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_pick_one_or_none() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_repeatable() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_optional() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_required() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_required_and_ordered() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_submotif_library() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_subset() (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) set_suffix() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) set_sugar() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_sugar_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_suite_cluster_radius() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_super_secret_fixed_interface_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_superimpose_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_suppress_checkpoints() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_suppress_zero_occ_pdb_output() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_sweep_nonpivot_torsions() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_sweep_nsteps() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_sweep_start_angle() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_sweep_step_size() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_sym_dof_names() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_symm_count() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_symm_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) set_symm_type() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_symmetric_sequence() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_tag_from_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_takeoff_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_takeoff_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_targ_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_targ_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_target() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_target_atom_name() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_target_geomcst_id() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_target_range() (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_target_res() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) set_target_res_index() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_target_res_pdb() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) set_target_residue() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_target_type() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) set_task() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter 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) set_task_and_movemap() (in module pyrosetta.rosetta.protocols.hydrate) set_task_factory() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector 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) set_task_scaling() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_task_with_de_novo_water_using_resfile() (in module pyrosetta.rosetta.protocols.hydrate) set_taskfactory() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_tau() (pyrosetta.rosetta.core.conformation.Residue method) set_temp() (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_temp_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_temperature() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_temperature_observer() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) set_temperature_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_temperature_schedule() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_tempering() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) set_template_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_template_res_index() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_temps() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_terminal_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_test_all_mg_hydration_frames() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_tether_jump() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_thermal_sampler_output_min_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_theta() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pose.Pose method) set_threshold() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) set_throw_on_double_registration() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) set_tilt() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_tilt1_center() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_tilt2_center() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_tmh_jump() (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) set_to_origin() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) set_to_pose() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) set_tolerance() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_tolerated_overlap() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_torsion() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) set_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) set_torsion_to_pose() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_torsion_type() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_total_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_total_jobs() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_total_residue() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_total_score_last_considered() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_total_weight() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_tracer_options() (pyrosetta.rosetta.basic.TracerImpl method) set_traits() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) set_traits_size() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) set_trans_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_translation() (pyrosetta.rosetta.core.kinematics.Jump method) set_translation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_trim_info() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_turn_off_rna_chem_map_during_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_two_stage_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_type() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.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.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover 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.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover 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.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) set_unbound_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_uniform_backrub() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_uniform_euler_angle_bin_width() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_uniform_sd_sampling() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) set_uniform_trans() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_uniform_xyz_bin_width() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_unweighted_function() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_up_mapfile_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) set_up_metal_bonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_up_metal_constraints() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_up_quota_nnmake_style() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_up_residuearrayannealableenergy_for_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) set_up_ss_abego_quota() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_up_target_sequence() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) set_up_voxel_grid_and_compute_burial() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_update_boinc() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) set_update_polymer_bond_dependent_atoms() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_update_polymer_dependent() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_upper_connect_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) set_upper_residues() (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) set_upper_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_upper_threshold() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_upper_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_upstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) set_use_basic_enhanced_n_linked_sequon() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_use_big_polar_hydrogen() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_use_centroid_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_cluster_csts() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_cluster_for_H3() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_conformer_population_stats() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_use_constraints() (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) set_use_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_use_coordinate_constraints() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_use_ddG_style() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_defaults() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) set_use_delta() (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) set_use_dssp_reduced() (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) set_use_ellipsoidal_randomization() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_use_epitope_constraints() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_use_general_csts_on_cluster_failure() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_green_packer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_use_harmonic_function() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_use_hbnet_behavior() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_increased_vdw_radii() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_use_jobname() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_legacy_protocol() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) set_use_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_use_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_use_outliers() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_use_packer_instead_of_rotamer_trials() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_use_pdb_format_HETNAM_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_use_phenix_geo() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_use_rama2b() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_use_rama_prepro_for_sampling() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_use_reporter_behavior() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_resfile() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_sc_neighbors() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_secondary_graft_mover_if_needed() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_use_seqprof_constraints() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) set_use_sugar_bb_data_if_needed() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_use_three_letter_code() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) set_use_tracer() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) set_use_vsasa() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_user_chain1() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_user_chain2() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_user_defined_name() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_user_input_VDW_bin_checker() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_user_provided_movers() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_using() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) set_using_a_resselect() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_valid() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) set_valid_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) set_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_value() (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression 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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) set_variant_type() (pyrosetta.rosetta.core.chemical.ResidueProperties method) set_vary_bondangles() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_vary_ca_bond_angles() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_vary_polar_hydrogen_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_vary_rna_bond_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_vdw_cached_rep_screen_info() (in module pyrosetta.rosetta.protocols.scoring) set_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) set_vdw_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) set_VDW_rep_alignment_RMSD_CUTOFF() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_VDW_rep_delete_matching_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_VDW_rep_screen_info() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_VDW_rep_screen_physical_pose_clash_dist_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_VDW_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_verbose() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_verbose_sampler() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_vertex_member_of_group() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_view() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_virtual_sugar_do_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_virtual_sugar_do_screens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_virtual_sugar_keep_base_fixed() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_virtual_sugar_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_virtualize_packable_moieties_in_screening_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_vlb() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) set_voxel_size_and_padding() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_water_info_and_add_de_novo_water() (in module pyrosetta.rosetta.protocols.hydrate) set_weak_pointer_to_self() (pyrosetta.rosetta.core.kinematics.AtomTree method) set_weight() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_weight_constraints_NtoC() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_weight_constraints_sheet() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_weight_if_zero() (pyrosetta.rosetta.core.scoring.ScoreFunction method) set_weights() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_width() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) set_window_size() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) set_working_moving_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) set_working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_working_parameters() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_working_parameters_exist() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_write_all_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_write_glycan_pdb_codes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_write_no_structures() (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_write_pdb_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_write_pdb_parametric_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_write_separate_scorefile() (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_wt_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_wu_type() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) set_x_standard_deviations() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_xyz() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) set_xyz_bin_widths() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_z0_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_z1_offset() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) set_zero_prob_weight_at() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_zeta() (pyrosetta.rosetta.core.pose.Pose method) setall() (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) SetAllAtomsRepulsive (class in pyrosetta.rosetta.core.chemical) SetAtomicCharge (class in pyrosetta.rosetta.core.chemical) SetAtomTree (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetAtomType (class in pyrosetta.rosetta.core.chemical) setB() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetBackboneHeavyatom (class in pyrosetta.rosetta.core.chemical) SetCatalyticResPackBehavior (class in pyrosetta.rosetta.protocols.enzdes) setCenterOnMiddleCA() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetChiMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) setClusterOversamp() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setClusterRadius() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setConvoluteSingleR() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setDelR() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setDoRefine() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetFormalCharge (class in pyrosetta.rosetta.core.chemical) setFragDens() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setGridStep() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetICoor (class in pyrosetta.rosetta.core.chemical) SetInterchangeabilityGroup_String (class in pyrosetta.rosetta.core.chemical) SetIO_String (class in pyrosetta.rosetta.core.chemical) setLaplacianOffset() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setMaxRotPerTrans() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetMembraneCenterMover (class in pyrosetta.rosetta.protocols.membrane) SetMembraneCenterMoverCreator (class in pyrosetta.rosetta.protocols.membrane) SetMembraneNormalMover (class in pyrosetta.rosetta.protocols.membrane) SetMembraneNormalMoverCreator (class in pyrosetta.rosetta.protocols.membrane) SetMembranePositionMover (class in pyrosetta.rosetta.protocols.membrane) SetMembranePositionMoverCreator (class in pyrosetta.rosetta.protocols.membrane) setMinBackbone() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setMinDist() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetMMAtomType (class in pyrosetta.rosetta.core.chemical) setNames() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) setNative() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetNbrAtom (class in pyrosetta.rosetta.core.chemical) SetNbrRadius (class in pyrosetta.rosetta.core.chemical) setNCyc() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setNeighbors() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) SetNetFormalCharge (class in pyrosetta.rosetta.core.chemical) setNormScores() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setNRsteps() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetOrientAtom (class in pyrosetta.rosetta.core.chemical) setOutputSilent() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setPassThrough() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setPdbCodes() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) setPointRadius() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetPolymerConnectAtom (class in pyrosetta.rosetta.core.chemical) setPoseExtraScore() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) SetResidueAliasMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) setResidueRange() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) SetSDFType() (pyrosetta.rosetta.core.chemical.Bond method) setSecStruct() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) setSeed() (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) setSymminfo() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) setTag() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetTemperatureFactor (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) setTopN() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) SetTorsion (class in pyrosetta.rosetta.protocols.simple_moves) SetToType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) setup() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) setup_A_LH_foldtree() (in module pyrosetta.rosetta.protocols.antibody) setup_after_edge_addition() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) setup_alignment_map() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) setup_atom_id_map() (in module pyrosetta.rosetta.core.pose.copydofs) setup_atom_id_map_match_atom_names() (in module pyrosetta.rosetta.core.pose.copydofs) setup_atom_type_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_atomic_charge_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_attlist_for_derived_classes() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) setup_base_pair_constraints() (in module pyrosetta.rosetta.core.pose.rna) setup_bulge_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_CDR_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) setup_CDR_clusters() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) setup_centroid_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_centroid_scatter() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) setup_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) setup_chain_break_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_chain_break_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) setup_chainbreak_variants() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) setup_coarse_chainbreak_constraints() (in module pyrosetta.rosetta.protocols.rna.denovo) setup_conformer_map() (in module pyrosetta.rosetta.protocols.motifs) setup_connectivity() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) setup_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_convergence_checks_from_cmdline() (in module pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) setup_copy_DOF_input() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_corresponding_atoms() (in module pyrosetta.rosetta.core.conformation) setup_cylindrical_coords() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) setup_default_evaluators() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) setup_disconnected() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_dof_mask_from_move_map() (in module pyrosetta.rosetta.core.pose) setup_dof_to_torsion_map() (in module pyrosetta.rosetta.core.pose) setup_element2name() (in module pyrosetta.rosetta.core.chemical.element) setup_empty_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_filter_stats() (in module pyrosetta.rosetta.protocols.ncbb) setup_fold() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) setup_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) setup_fold_tree_and_jumps_and_variants() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) setup_foldtree() (in module pyrosetta.rosetta.protocols.docking) setup_foldtree_around_anchor_invrot() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) setup_foldtree_from_anchors() (in module pyrosetta.rosetta.protocols.membrane) setup_foldtree_pose_com() (in module pyrosetta.rosetta.protocols.membrane) setup_for_density_scoring() (in module pyrosetta.rosetta.core.import_pose) setup_for_derivatives() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_derivatives_for_residue() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) setup_for_derivatives_for_residue_pair() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) setup_for_dna() (in module pyrosetta.rosetta.protocols.relax) setup_for_lr2benmeth_minimization_for_respair() (pyrosetta.rosetta.core.scoring.ScoreFunction method) setup_for_minimizing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_minimizing_for_node() (pyrosetta.rosetta.core.scoring.ScoreFunction method) setup_for_minimizing_for_residue() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) setup_for_minimizing_for_residue_pair() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) setup_for_minimizing_sr2b_enmeths_for_minedge() (pyrosetta.rosetta.core.scoring.ScoreFunction method) setup_for_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_residue_pair_energies() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) setup_for_sampling() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) setup_for_scoring() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_scoring_for_residue() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) setup_for_scoring_for_residue_energy_methods() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) setup_for_scoring_for_residue_pair() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) setup_form_factors() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) setup_fragment_picker() (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) setup_from_kill_hairpins_file() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_from_psipred() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_from_rotamer_dots() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) setup_full_model_info() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) setup_fullatom_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_glycan_nodes() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) setup_glycan_trees() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) setup_icoor_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_info() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) setup_jumps() (in module pyrosetta.rosetta.core.import_pose) setup_kic_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_kic_with_fragments_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_killhairpins() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_LH_A_foldtree() (in module pyrosetta.rosetta.protocols.antibody) setup_list() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) setup_loophash_kic_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_matching_atoms_with_given_names() (in module pyrosetta.rosetta.core.scoring) setup_matching_CA_atoms() (in module pyrosetta.rosetta.core.scoring) setup_matching_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) setup_matching_protein_backbone_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) setup_membrane_topology() (in module pyrosetta.rosetta.protocols.relax) setup_min_map() (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) setup_movemap() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) setup_native_pose() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) setup_options_for_VDW_bin_checker() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) setup_packer() (in module pyrosetta.rosetta.protocols.mpi_refinement) setup_packer_and_movemap() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) setup_packer_task() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) setup_parallel_antiparallel_weights() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) setup_pert_foldtree() (in module pyrosetta.rosetta.protocols.ncbb) setup_pose_from_rbsegs() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_pose_input_stream() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) setup_pose_rbsegs_keep_loops() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_pose_setup_class() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_pose_with_moving_residue_alternative_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) setup_protein_backbone_atom_id_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) setup_rmsd_atom_names() (in module pyrosetta.rosetta.protocols.analysis.simple_metrics) setup_rna_working_parameters() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_rsdtype() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) setup_sampler() (in module pyrosetta.rosetta.protocols.stepwise.sampler.rna) setup_simple_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) setup_simple_full_length_rna_working_parameters() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_single_loop_double_arm_remodeling_foldtree() (in module pyrosetta.rosetta.protocols.grafting) setup_single_loop_single_arm_remodeling_foldtree() (in module pyrosetta.rosetta.protocols.grafting) setup_star_topology() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_suite_atom_id_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) setup_symmetric_conformation() (in module pyrosetta.rosetta.core.conformation.symmetry) setup_three_prime_phosphate_based_on_next_residue() (in module pyrosetta.rosetta.core.pose.rna) setup_unified_stepwise_modeler() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) setup_user_coordinate_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_user_defined_jumps() (in module pyrosetta.rosetta.core.import_pose) setup_vall_cheating_fragments() (in module pyrosetta.rosetta.protocols.frags) setup_vall_fragments() (in module pyrosetta.rosetta.protocols.frags) setup_vary_polar_hydrogen_geometry() (in module pyrosetta.rosetta.protocols.simple_moves) setup_vary_rna_bond_geometry() (in module pyrosetta.rosetta.protocols.simple_moves) setup_vdw_cached_rep_screen_info() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) setup_water_bank_for_magnesiums() (in module pyrosetta.rosetta.core.import_pose) setup_working_parameters_explicit() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) setup_working_parameters_for_swa() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) SetupForFibrilMover (class in pyrosetta.rosetta.protocols.fibril) SetupForSymmetryMover (class in pyrosetta.rosetta.protocols.symmetry) SetupMetalsMover (class in pyrosetta.rosetta.protocols.simple_moves) SetupNCSMover (class in pyrosetta.rosetta.protocols.symmetry) SetupRamaTables() (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) SetVirtualShadow (class in pyrosetta.rosetta.core.chemical) sever_chemical_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) SewGraph (class in pyrosetta.rosetta.protocols.legacy_sewing) sfd_req_1benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfd_req_1benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfd_req_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfd_req_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) sformat_idxof() (in module pyrosetta.rosetta.numeric.random) sfr() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) sfs_dm_req_1benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_dm_req_1benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_dm_req_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_dm_req_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_drs_req_enmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_drs_req_enmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) sfs_req_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) sfs_req_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) sgn() (in module pyrosetta.rosetta.core.io.pose_from_sfr) ShapeComplementarityCalculator (class in pyrosetta.rosetta.core.scoring.sc) ShapeComplementarityCalculatorException (class in pyrosetta.rosetta.core.scoring.sc) share_axis_atoms() (in module pyrosetta.rosetta.core.scoring.power_diagram) shared_from_this() (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) SharedSilentDataType (class in pyrosetta.rosetta.core.io.silent) ShearFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) ShearMinCCDTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) ShearMover (class in pyrosetta.rosetta.protocols.simple_moves) sheet_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) SheetBuilder (class in pyrosetta.rosetta.protocols.jumping) SheetDB (class in pyrosetta.rosetta.protocols.denovo_design.components) SheetFoldType (class in pyrosetta.rosetta.protocols.fldsgn.topology) SheetFoldTypeManager (class in pyrosetta.rosetta.protocols.fldsgn.topology) SHEETInformation (class in pyrosetta.rosetta.core.io) SHEETInformations() (pyrosetta.rosetta.core.io.StructFileRep method) SheetRemodelConstraintGenerator (class in pyrosetta.rosetta.protocols.fldsgn) SheetTranslate (class in pyrosetta.rosetta.protocols.nonlocal) shell_radius_for_atom() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) shift() (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) shift_by() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) shift_jump_numbers_in_dofs() (in module pyrosetta.rosetta.core.conformation.symmetry) shift_jumps() (in module pyrosetta.rosetta.protocols.forge.methods) shift_to() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) short_desc() (pyrosetta.rosetta.core.pose.PDBInfo method) short_description() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) short_frag_cycle_ratio() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) short_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) short_ss_loop_filter() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) shortd() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) ShortToRealAngle() (in module pyrosetta.rosetta.protocols.loophash) show() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint 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.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.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.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.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.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover 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.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover 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.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_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.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackPwatRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) show_accessed_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_additional() (pyrosetta.rosetta.core.scoring.ScoreFunction method) show_additional_info() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPHelicalityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.util_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) show_all() (pyrosetta.rosetta.utility.options.OptionCollection method) show_all_atom_names() (pyrosetta.rosetta.core.chemical.ResidueType method) show_all_fixes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) show_all_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_all_residue_tasks() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) show_atom_tree() (in module pyrosetta.rosetta.core.conformation) show_availability() (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) show_base_pair_params() (in module pyrosetta.rosetta.core.scoring.dna) show_classic() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) show_cluster_assignments() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) show_counters() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) show_def() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) show_definition() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) show_definitions() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) show_dna_geometry() (in module pyrosetta.rosetta.core.scoring.dna) show_foldtree() (in module pyrosetta.rosetta.core.conformation.symmetry) show_header() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) show_help() (pyrosetta.rosetta.utility.options.OptionCollection method) show_help_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_if_nonzero_weight() (pyrosetta.rosetta.core.scoring.EMapVector method) show_inaccessed_user_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_internals() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) show_line() (pyrosetta.rosetta.core.scoring.ScoreFunction method) show_line_headers() (pyrosetta.rosetta.core.scoring.ScoreFunction method) show_new_base_step_params() (in module pyrosetta.rosetta.core.scoring.dna) show_nonzero() (pyrosetta.rosetta.core.scoring.EMapVector method) show_numbers() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) show_option_help() (pyrosetta.rosetta.utility.options.OptionCollection method) show_option_help_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_params() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) show_pdb_ids() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) show_pretty() (pyrosetta.rosetta.core.scoring.ScoreFunction method) show_rdc_values() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_residue_connections() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) show_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) show_scorefxn_weight_lines() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) show_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) show_scoring_methods() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) show_state() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) show_submotif_info_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) show_table_text() (pyrosetta.rosetta.utility.options.OptionCollection method) show_table_Wiki() (pyrosetta.rosetta.utility.options.OptionCollection method) show_tensor_matrix() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_tensor_stats() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_tensor_stats_nls() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_time() (in module pyrosetta.rosetta.basic) show_total_headers() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) show_totals() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) show_unmoved() (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) show_unused_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_user() (pyrosetta.rosetta.utility.options.OptionCollection method) show_valid() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) show_violations() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) show_water_hb_network() (in module pyrosetta.rosetta.protocols.hydrate) show_weighted() (pyrosetta.rosetta.core.scoring.EMapVector method) ShowHState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) shrink() (pyrosetta.rosetta.protocols.frags.VallData method) shrink_to_fit() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) shuffle() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) shutdown() (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) sidechain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) sidechain_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) sidechain_sidechain_energy() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) sidechainAtoms_begin() (pyrosetta.rosetta.core.conformation.Residue method) SidechainContactDistCutoff (class in pyrosetta.rosetta.protocols.frag_picker) SidechainMCMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainMetropolisHastingsMover (class in pyrosetta.rosetta.protocols.canonical_sampling) SidechainMetropolisHastingsMoverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) SidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainMoverBase (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainStateAssignment (class in pyrosetta.rosetta.core.pack.scmin) sigma1() (pyrosetta.rosetta.core.scoring.CSA method) sigma2() (pyrosetta.rosetta.core.scoring.CSA method) sigma3() (pyrosetta.rosetta.core.scoring.CSA method) Sigmoid (class in pyrosetta.rosetta.protocols.calc_taskop_filters) sigmoid_filter() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) sign() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) signature_string() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) silent() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) silent_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) silent_Es() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) silent_file() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) silent_file_data() (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) silent_in() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) silent_out() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) silent_struct_output_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) SilentEnergy (class in pyrosetta.rosetta.core.io.silent) SilentFileData (class in pyrosetta.rosetta.core.io.silent) SilentFileHeaderLine (class in pyrosetta.rosetta.core.io.silent) SilentFileJobInputter (class in pyrosetta.rosetta.protocols.jd2) SilentFileJobOutputter (class in pyrosetta.rosetta.protocols.jd2) SilentStruct (class in pyrosetta.rosetta.core.io.silent) SilentStructCreator (class in pyrosetta.rosetta.core.io.silent) SilentTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) SilentTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) SIMPLE_CYCPEP_PREDICT_MPI_SORT_TYPE (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) simple_element_naming_func_has_been_set() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) simple_fold_tree() (in module pyrosetta.rosetta.protocols.antibody) (in module pyrosetta.rosetta.protocols.antibody_legacy) (in module pyrosetta.rosetta.protocols.star) simple_ft() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) simple_mapping_from_file() (in module pyrosetta.rosetta.core.sequence) simple_metric_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) simple_numeric_deriv_check() (in module pyrosetta.rosetta.core.optimization) simple_one_loop_fold_tree() (in module pyrosetta.rosetta.protocols.antibody) (in module pyrosetta.rosetta.protocols.antibody_legacy) simple_rmsd_cutoff_relax() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) simple_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) simple_visualize_fold_tree() (in module pyrosetta.rosetta.core.kinematics) simple_visualize_fold_tree_and_movemap() (in module pyrosetta.rosetta.core.kinematics) simple_visualize_fold_tree_and_movemap_bb_chi() (in module pyrosetta.rosetta.core.kinematics) SimpleCycpepPredictApplication (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) SimpleCycpepPredictApplication_MPI_JobResultsSummary (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) SimpleGlycosylateMover (class in pyrosetta.rosetta.protocols.carbohydrates) SimpleHbondsToAtomFilter (class in pyrosetta.rosetta.protocols.simple_filters) SimpleInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) SimpleMetric (class in pyrosetta.rosetta.core.simple_metrics) SimpleMetricFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SimpleMetricFilter (class in pyrosetta.rosetta.protocols.simple_filters) SimpleMetricLoader (class in pyrosetta.rosetta.protocols.parser) SimpleThreadingMover (class in pyrosetta.rosetta.protocols.simple_moves) simplifyWhiteSpace() (in module pyrosetta.rosetta.protocols.sparta) simulate_mpi() (pyrosetta.rosetta.utility.SimulateMPI method) simulate_mpi_message_type (class in pyrosetta.rosetta.utility) SimulatedTempering (class in pyrosetta.rosetta.protocols.canonical_sampling) SimulatedTemperingCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) SimulateMPI (class in pyrosetta.rosetta.utility) simultaneous_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) sin_cos_range() (in module pyrosetta.rosetta.numeric) SINFXN() (in module pyrosetta.rosetta.numeric.crick_equations) single_beta_sample() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) single_ligand_motif_from_stream() (in module pyrosetta.rosetta.protocols.motifs) single_motif_from_filename() (in module pyrosetta.rosetta.protocols.motifs) single_motif_from_stream() (in module pyrosetta.rosetta.protocols.motifs) single_residue_from_stream() (in module pyrosetta.rosetta.protocols.motifs) single_state_design() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) single_user_input_chunk() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) SingleBasicRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleDownstreamResidueWriter (class in pyrosetta.rosetta.protocols.match.output) SingleFileBuffer (class in pyrosetta.rosetta.protocols.jd2) SingleLigandRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleResidueCenrotLibrary (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) SingleResidueFragData (class in pyrosetta.rosetta.core.fragment) SingleResidueMultifunc (class in pyrosetta.rosetta.core.optimization) SingleResidueRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleResidueTorsionFragmentLibrary (class in pyrosetta.rosetta.protocols.frags) SiteConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) SiteConstraintResiduesCreator (class in pyrosetta.rosetta.core.scoring.constraints) SixDCoordinateBinner (class in pyrosetta.rosetta.numeric.geometry.hashing) SixDOffsetTree (class in pyrosetta.rosetta.numeric.geometry.hashing) size() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList 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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) size1() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) size2() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) size_col() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) size_constraint_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) size_left() (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) size_of_query() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) sized() (in module pyrosetta.rosetta.ObjexxFCL) skip() (in module pyrosetta.rosetta.ObjexxFCL.format) (in module pyrosetta.rosetta.utility.io) skip_chi_min() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) skip_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) skip_coord_constraints() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) skip_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) skip_rate() (pyrosetta.rosetta.protocols.loops.Loop method) skip_redundant_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) skip_set_reasonable_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) slice() (in module pyrosetta.rosetta.protocols.stepwise.modeler) slice_1base_indicies() (in module pyrosetta.bindings.utility) slice_out_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) slice_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) slide_axis() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) slide_back_to_origin() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) slide_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) slide_into_contact() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) slide_into_contact_and_score() (in module pyrosetta.rosetta.protocols.sic_dock) slide_into_contact_and_score_DEPRICATED() (in module pyrosetta.rosetta.protocols.sic_dock) slide_jump() (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.core.kinematics.FoldTree method) SlideCriteriaType (class in pyrosetta.rosetta.core.conformation.symmetry) SlideIntoContact (class in pyrosetta.rosetta.protocols.docking) SlideType (class in pyrosetta.rosetta.core.conformation.symmetry) slurp() (in module pyrosetta.rosetta.utility) SmallBBSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) smallest_ring_size() (pyrosetta.rosetta.core.chemical.ResidueType method) smallmer_from_largemer() (in module pyrosetta.rosetta.protocols.forge.methods) SmallMinCCDTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) SmallMover (class in pyrosetta.rosetta.protocols.simple_moves) smooth_fa_elec() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) smooth_move_small() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) smooth_to_zero() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) SmoothEnvPairPotential (class in pyrosetta.rosetta.core.scoring) SmoothPolicy (class in pyrosetta.rosetta.protocols.nonlocal) SmoothSymmetricFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) SmotifFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SnugDock (class in pyrosetta.rosetta.protocols.antibody.snugdock) SoedingFunc (class in pyrosetta.rosetta.core.scoring.func) sog_cst_param() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) SOGFunc (class in pyrosetta.rosetta.core.scoring.func) SOGFunc_Impl (class in pyrosetta.rosetta.core.scoring.func) sol_weight() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) SolutionPicker (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) solv1() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) solv2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) solve() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) solve_gaps() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) solve_sturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) SolventAccessibility (class in pyrosetta.rosetta.protocols.frag_picker.scores) solvF2BR() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) solvF2d() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) sort() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) sort_by() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) sort_by_second() (in module pyrosetta.rosetta.protocols.ligand_docking) sort_by_weighted_energy() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) sort_new_rotamers_into_rotset_vector() (in module pyrosetta.rosetta.core.pack.rotamer_set) sort_pair_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) sort_pose_by_score() (in module pyrosetta.rosetta.core.pose) sort_R_function() (pyrosetta.rosetta.core.optimization.EItem method) sort_residue_type_pointers_by_name() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) sort_seq_num_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) sort_silent_scores() (pyrosetta.rosetta.core.io.silent.SilentStruct method) sorted_res_list() (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) sorted_values() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) source_chain() (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) source_file_name() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) source_filename() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) source_id_is_mapped() (pyrosetta.rosetta.utility.subset_mapping method) source_pose() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) source_size() (pyrosetta.rosetta.utility.subset_mapping method) sources_same() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) space() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.ObjexxFCL.format) space_prefixed() (pyrosetta.rosetta.utility.options.OptionCollection method) SpacegroupSetting (class in pyrosetta.rosetta.protocols.cryst) spacing() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) spairs_from_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) span_file() (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) spanfile() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) spanfile_name() (in module pyrosetta.rosetta.core.conformation.membrane) spanfile_names() (in module pyrosetta.rosetta.core.conformation.membrane) spanning() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) spanning_topology() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) spearman() (in module pyrosetta.rosetta.protocols.ligand_docking) SpecialSegmentsObserver (class in pyrosetta.rosetta.core.pose.datacache) specified_check() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) specified_report() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) sphere_lookup() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) spheremode (class in pyrosetta.rosetta.protocols.viewer) spherical() (in module pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) (pyrosetta.rosetta.core.kinematics.Stub method) spin_axis() (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) spin_id() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) spin_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) SpinAroundPartnerMoverCreator (class in pyrosetta.rosetta.protocols.membrane) spline_by_z() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) spline_coeffs() (in module pyrosetta.rosetta.core.scoring.electron_density) spline_from_file() (in module pyrosetta.rosetta.numeric.interpolation) spline_interpolate() (in module pyrosetta.rosetta.numeric.interpolation.spline) spline_second_derivative() (in module pyrosetta.rosetta.numeric.interpolation.spline) SplineParameters (class in pyrosetta.rosetta.core.scoring.etable) split() (in module pyrosetta.rosetta.protocols.sparta) (in module pyrosetta.rosetta.utility) split_by_ca_ca_dist() (in module pyrosetta.rosetta.protocols.loops) split_by_chain() (pyrosetta.rosetta.core.pose.Pose method) split_by_newlines() (in module pyrosetta.rosetta.utility) split_by_resSeq() (in module pyrosetta.rosetta.protocols.loops) split_existing_edge_at_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) split_line_to_polyval() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) split_line_to_spline() (pyrosetta.rosetta.core.scoring.membrane.MPResidueLipophilicityEnergy method) split_mid_ranges() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) split_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) split_sequence_motif() (in module pyrosetta.rosetta.core.sequence) split_to_list() (in module pyrosetta.rosetta.utility) split_to_set() (in module pyrosetta.rosetta.utility) split_topology_by_jump() (in module pyrosetta.rosetta.protocols.membrane) split_topology_by_jump_noshift() (in module pyrosetta.rosetta.protocols.membrane) split_unfolded_label_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) split_unfolded_value_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) split_up_remark_line() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) split_WhiteSpace() (in module pyrosetta.rosetta.protocols.sparta) split_whitespace() (in module pyrosetta.rosetta.utility) SplitAndMixPoseMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) sq_vec_distance() (in module pyrosetta.rosetta.numeric.kdtree) sqr() (in module pyrosetta.rosetta.numeric.interpolation.spline) square() (in module pyrosetta.rosetta.ObjexxFCL) square_distance() (pyrosetta.rosetta.core.scoring.EnergyEdge method) src_pose() (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) src_pose_start() (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) SS() (in module pyrosetta.rosetta.ObjexxFCL.format) ss() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ss_element_id() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) ss_index() (in module pyrosetta.rosetta.protocols.frag_picker.quota) SS_Info (class in pyrosetta.rosetta.core.scoring) SS_Info2 (class in pyrosetta.rosetta.protocols.fldsgn.topology) SS_Killhairpins_Info (class in pyrosetta.rosetta.core.scoring) ss_length_check() (in module pyrosetta.rosetta.protocols.frags) ss_penalty() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) ss_str() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ssbond_map() (pyrosetta.rosetta.core.io.StructFileRep method) SSBondInformation (class in pyrosetta.rosetta.core.io) SSElementSelector (class in pyrosetta.rosetta.core.select.residue_selector) SSManager (class in pyrosetta.rosetta.core.sequence) SSPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) SSType (class in pyrosetta.rosetta.protocols.comparative_modeling.features) st_atr() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) st_rep() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) st_sol() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) stage1_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) stage2_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) stage3_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) stage4_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) stage5_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) StageID (class in pyrosetta.rosetta.protocols.abinitio) (class in pyrosetta.rosetta.protocols.abinitio.abscript) standard_RG (class in pyrosetta.rosetta.numeric.random) StandardDisulfPairingLibrary (class in pyrosetta.rosetta.protocols.jumping) StandardJobQueen (class in pyrosetta.rosetta.protocols.jd3.standard) StandardPairingLibrary (class in pyrosetta.rosetta.protocols.jumping) StandardPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) Star (class in pyrosetta.rosetta.ObjexxFCL) star_fold_tree() (in module pyrosetta.rosetta.protocols.protein_interface_design) StarAbinitio_main() (in module pyrosetta.rosetta.protocols.star) start() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment 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.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) start_atom() (pyrosetta.rosetta.core.kinematics.Edge method) start_atomid() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atomid1() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atomid2() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atoms1() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atoms2() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_doc() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_evaluation_timer() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) start_file() (in module pyrosetta.rosetta.basic.options) start_files() (in module pyrosetta.rosetta.basic.options) start_from_centroid() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) start_key() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) start_list() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) start_map() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_new_batch() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) start_res() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) start_seq2() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) start_time() (pyrosetta.rosetta.protocols.jd2.Job method) start_timing() (pyrosetta.rosetta.protocols.jd2.Job method) start_tree_at_chain() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) starting_node() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) starting_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) startswith() (in module pyrosetta.rosetta.utility) startup() (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) state() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) state_momento() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) state_unassigned() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) states() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) StaticIndexRange (class in pyrosetta.rosetta.ObjexxFCL) statistics_valid() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) StatsType (class in pyrosetta.rosetta.protocols.moves) status() (pyrosetta.rosetta.protocols.jd3.JobResult method) status_prefix() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) status_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) steal() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) steal_alignment() (in module pyrosetta.rosetta.core.sequence) steal_constant_length_frag_set_from_pose() (in module pyrosetta.rosetta.core.fragment) steal_def() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) steal_def_clone() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) steal_frag_set_from_pose() (in module pyrosetta.rosetta.core.fragment) steal_inversion() (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) steal_ligands() (in module pyrosetta.rosetta.protocols.comparative_modeling) steepness() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) step() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) step_count() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) step_size() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) stepsize() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) stepwise_addable_pose_residue() (in module pyrosetta.rosetta.core.pose) stepwise_addable_residue() (in module pyrosetta.rosetta.core.pose) StepWiseLegacyClusterer (class in pyrosetta.rosetta.protocols.stepwise.modeler.align) StepWiseLegacyClustererSilentBased (class in pyrosetta.rosetta.protocols.stepwise.modeler.align) StepWiseModelerOptions (class in pyrosetta.rosetta.protocols.stepwise.modeler.options) StepWiseMove (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) StepWisePacker (class in pyrosetta.rosetta.protocols.stepwise.modeler.packer) StepWiseProteinBackboneSampler (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) StepWiseProteinCCD_Closer (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) StepWiseProteinKIC_LoopBridger (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) StepWiseProteinMinimizer (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) StepWiseProteinPoseSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) StepWiseRNA_Clusterer (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) StepWiseRNA_PoseSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) StepWiseScreenerType (class in pyrosetta.rosetta.protocols.stepwise.screener) StepWiseWorkingParametersSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) still_interested() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) stop() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) stop_at_closure() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) stop_atom() (pyrosetta.rosetta.core.kinematics.Edge method) stop_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) stop_res() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) stop_sampling() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) stopping_condition() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) store_active_energies() (pyrosetta.rosetta.core.scoring.EnergyEdge method) store_argv_in_file() (pyrosetta.rosetta.core.io.silent.SilentFileData method) store_base_residue_type_name_in_sfr() (in module pyrosetta.rosetta.core.io.pdb) store_classification() (pyrosetta.rosetta.core.io.HeaderInformation method) store_compound() (pyrosetta.rosetta.core.io.HeaderInformation method) store_connection_architect() (in module pyrosetta.rosetta.protocols.denovo_design.connection) store_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) store_CSA_in_pose() (in module pyrosetta.rosetta.core.scoring) store_current_derivatives() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) store_DC_in_pose() (in module pyrosetta.rosetta.core.scoring) store_denovo_architect() (in module pyrosetta.rosetta.protocols.denovo_design.architects) store_deposition_date() (pyrosetta.rosetta.core.io.HeaderInformation method) store_experimental_technique() (pyrosetta.rosetta.core.io.HeaderInformation method) store_experimental_techniques() (pyrosetta.rosetta.core.io.HeaderInformation method) store_H3_cter_fragment() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) store_idCode() (pyrosetta.rosetta.core.io.HeaderInformation method) store_keywords() (pyrosetta.rosetta.core.io.HeaderInformation method) store_line() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) store_new_sphere() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) store_RDC_in_pose() (in module pyrosetta.rosetta.core.scoring) store_RDC_ROHL_in_pose() (in module pyrosetta.rosetta.core.scoring) store_RDC_segments_in_pose() (in module pyrosetta.rosetta.protocols.scoring) store_title() (pyrosetta.rosetta.core.io.HeaderInformation method) store_trie() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) store_xyz() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) StoreCombinedStoredTasksMover (class in pyrosetta.rosetta.protocols.task_operations) stored_data() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) stored_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) stored_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) StoredResidueSubsetSelector (class in pyrosetta.rosetta.protocols.residue_selectors) StoredRotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) StorePoseSnapshot (class in pyrosetta.rosetta.protocols.simple_moves) StoreResidueSubsetMover (class in pyrosetta.rosetta.protocols.residue_selectors) stores_residue_map() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) StoreTaskMover (class in pyrosetta.rosetta.protocols.task_operations) str() (pyrosetta.rosetta.basic.datacache.CacheableString method) str_dn() (in module pyrosetta.rosetta.ObjexxFCL) str_dncase() (in module pyrosetta.rosetta.ObjexxFCL) str_up() (in module pyrosetta.rosetta.ObjexxFCL) str_upcase() (in module pyrosetta.rosetta.ObjexxFCL) Strand (class in pyrosetta.rosetta.protocols.fldsgn.topology) strand() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) strand_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) strand_id() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) strand_id1() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) strand_id2() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) strand_pairing() (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) strand_pairing_set() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) strand_pairings() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) StrandArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) StrandBundleFeaturesCreator (class in pyrosetta.rosetta.protocols.features.strand_assembly) StrandCurvatureByLevels (class in pyrosetta.rosetta.protocols.fldsgn.filters) StrandHelixGeometryFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) StrandOrientation (class in pyrosetta.rosetta.protocols.denovo_design.components) StrandPairing (class in pyrosetta.rosetta.core.scoring.dssp) StrandPairingSet (class in pyrosetta.rosetta.core.scoring.dssp) (class in pyrosetta.rosetta.protocols.fldsgn.topology) Strands (class in pyrosetta.rosetta.core.scoring) strands() (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) StrandTwistingMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) Strategy (class in pyrosetta.rosetta.core.conformation) strategy() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) stream() (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) streams_from_cmd_line() (in module pyrosetta.rosetta.core.import_pose.pose_stream) strict_column_mode() (pyrosetta.rosetta.core.io.silent.SilentFileData method) strict_looprelax_checks() (pyrosetta.rosetta.protocols.loops.Loops method) strict_lower() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) strict_upper() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) stride() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) string2float() (in module pyrosetta.rosetta.utility) string2int() (in module pyrosetta.rosetta.utility) string2Real() (in module pyrosetta.rosetta.utility) string2Size() (in module pyrosetta.rosetta.utility) string2uint() (in module pyrosetta.rosetta.utility) string_blosum() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) string_contains_gt_lt_or_ampersand() (in module pyrosetta.rosetta.utility.tag) string_from_property() (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) string_from_type_set_mode() (in module pyrosetta.rosetta.core.chemical) string_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) string_path() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) string_properties() (pyrosetta.rosetta.core.chemical.ResidueProperties method) string_rep() (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) string_split() (in module pyrosetta.rosetta.utility) string_split_multi_delim() (in module pyrosetta.rosetta.utility) string_split_simple() (in module pyrosetta.rosetta.utility) string_to_compound_token() (pyrosetta.rosetta.core.io.HeaderInformation method) string_to_experimental_technique() (pyrosetta.rosetta.core.io.HeaderInformation method) string_to_hb_eval_type() (in module pyrosetta.rosetta.core.scoring.hbonds) string_to_int() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) string_to_real() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) string_to_sha1() (in module pyrosetta.rosetta.utility) string_value() (pyrosetta.rosetta.core.io.silent.SilentEnergy method) stringafteroption() (in module pyrosetta.rosetta.basic.options) StringMetric (class in pyrosetta.rosetta.core.simple_metrics) StringOption (class in pyrosetta.rosetta.utility.options) StringOptionKey (class in pyrosetta.rosetta.utility.options) StringResourceStream (class in pyrosetta.rosetta.basic.resource_manager.locator) StringVectorOption (class in pyrosetta.rosetta.utility.options) StringVectorOptionKey (class in pyrosetta.rosetta.utility.options) strip() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) strip_out_magnesiums() (in module pyrosetta.rosetta.protocols.magnesium) strip_rotamer_library_specification() (pyrosetta.rosetta.core.chemical.ResidueType method) strip_spacers() (in module pyrosetta.rosetta.core.sequence) strip_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) stripped() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) stripped_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) StrongWolfe() (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) StrongWolfeLineMinimization (class in pyrosetta.rosetta.core.optimization) struct_from_job() (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) struct_ids_from_tag() (in module pyrosetta.rosetta.protocols.features) StructFileRep (class in pyrosetta.rosetta.core.io) StructFragmentMoverCreator (class in pyrosetta.rosetta.protocols.struct_fragment) structure_has_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) structure_list() (pyrosetta.rosetta.core.io.silent.SilentFileData method) structure_moved() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) StructureArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) StructureDataFactory (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureDataObserver (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureDataPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureFeaturesCreator (class in pyrosetta.rosetta.protocols.features) StructureScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) StructureSimilarityEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) Stub (class in pyrosetta.rosetta.core.kinematics) stub_atom() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) stub_atom1() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom1_id() (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) stub_atom2() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom2_id() (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) stub_atom3() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom3_id() (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) stub_defined() (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) stub_from_id() (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.core.pose.Pose method) stub_from_points() (in module pyrosetta.rosetta.protocols.hotspot_hashing) stub_id_to_named_stub_id() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) stub_minimize_movers() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) stub_sets() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) stub_tgt_angle() (in module pyrosetta.rosetta.protocols.hotspot_hashing) stub_to_points() (in module pyrosetta.rosetta.protocols.hotspot_hashing) StubID (class in pyrosetta.rosetta.core.id) StubMode (class in pyrosetta.rosetta.protocols.cyclic_peptide) StubStatus (class in pyrosetta.rosetta.protocols.hotspot_hashing) StubStubType (class in pyrosetta.rosetta.core.pose.rna) sub_rank() (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) sub_to_full() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) subdir() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) subelement_behavior() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) subelement_ct_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) submotif_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_info_containing_residues() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_info_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_library() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) submotif_tag() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) SubMotifInfo (class in pyrosetta.rosetta.core.pose.full_model_info) submover() (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) subset() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) subset_mapping (class in pyrosetta.rosetta.utility) substate() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) substitute_residue() (in module pyrosetta.rosetta.protocols.dna) substitution_group() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) subtract_chi_angles() (in module pyrosetta.rosetta.core.pack.dunbrack) subtract_degree_angles() (in module pyrosetta.rosetta.basic) subtract_radian_angles() (in module pyrosetta.rosetta.basic) success() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) suffix() (pyrosetta.rosetta.utility.options.OptionCollection method) suffix_from_jd_with_sep() (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) sugar_modifications_from_suffix() (in module pyrosetta.rosetta.core.io.carbohydrates) SugarBackboneEnergy (class in pyrosetta.rosetta.core.scoring.methods.carbohydrates) SugarBackboneEnergyCreator (class in pyrosetta.rosetta.core.scoring.methods.carbohydrates) SugarBBSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) SugarModificationsNomenclatureTableRow (class in pyrosetta.rosetta.core.chemical.carbohydrates) suggest_residue_number() (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.SidechainMoverBase method) suite_rmsd() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) suite_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) sum() (pyrosetta.rosetta.core.scoring.EMapVector method) sum_constraint_scoreterms() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) sum_energies() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) sum_total_residue_energy() (in module pyrosetta.rosetta.protocols.protein_interface_design) super_mute() (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) super_twiddles() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) superimpose_all() (in module pyrosetta.rosetta.protocols.mpi_refinement) superimpose_overhangs_heavy() (in module pyrosetta.rosetta.protocols.grafting) superimpose_pose() (in module pyrosetta.rosetta.core.scoring) superimpose_pose_legacy() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) superimpose_pose_on_subset_bb() (in module pyrosetta.rosetta.protocols.fibril) superimpose_pose_on_subset_CA() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) superimpose_to_single_user_input_chunk() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) superimpose_with_stepwise_aligner() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) SuperimposeMover (class in pyrosetta.rosetta.protocols.simple_moves) superposition_transform() (in module pyrosetta.rosetta.protocols.seeded_abinitio) (in module pyrosetta.rosetta.protocols.toolbox) suppress_CSI_codes() (pyrosetta.rosetta.utility.CSI_Sequence method) suppress_zero_occ_pdb_output() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) surface_exposed_nb_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) SurfaceEnergies (class in pyrosetta.rosetta.core.scoring.solid_surface) SurfaceEnergy (class in pyrosetta.rosetta.core.pack.interaction_graph) SurfacePotential (class in pyrosetta.rosetta.core.pack.interaction_graph) SurfaceVectorLoader (class in pyrosetta.rosetta.protocols.surface_docking) SurrogateVariableExpression (class in pyrosetta.rosetta.protocols.pack_daemon) svdcmp() (in module pyrosetta.rosetta.numeric.linear_algebra) SW() (in module pyrosetta.rosetta.ObjexxFCL.format) swap() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.std) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) swap4_aligned() (in module pyrosetta.rosetta.utility) swap_coordinates_in_pose() (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) swap_in() (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) swap_in_movemap() (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) swap_no_notify() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) swap_transform() (in module pyrosetta.rosetta.core.pose) sweep_incomplete() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) switch_conformer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) switch_focus_among_poses_randomly() (in module pyrosetta.rosetta.protocols.stepwise.modeler) switch_focus_to_other_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) switch_movemap() (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) switch_residue_type_set() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) switch_to_centroid_rot_set() (in module pyrosetta.rosetta.core.util) switch_to_fullatom() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) switch_to_residue_type_set() (in module pyrosetta.rosetta.core.util) SwitchMover (class in pyrosetta.rosetta.protocols.moves) SwitchResidueTypeSetMover (class in pyrosetta.rosetta.protocols.simple_moves) sym_dof_jump_num() (in module pyrosetta.rosetta.core.pose.symmetry) sym_dof_name() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) sym_dof_names() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) SymAtomTreeMinimizer (class in pyrosetta.rosetta.core.optimization.symmetry) SymAtomTreeMultifunc (class in pyrosetta.rosetta.core.optimization.symmetry) symbol2index() (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.SSManager method) symbolString2base5index() (pyrosetta.rosetta.core.sequence.ABEGOManager method) symbolString2index() (pyrosetta.rosetta.core.sequence.SSManager method) SymDock_main() (in module pyrosetta.rosetta.protocols.symmetric_docking) SymDockingSlideIntoContact (class in pyrosetta.rosetta.protocols.symmetry) SymDockProtocol (class in pyrosetta.rosetta.protocols.symmetric_docking) SymDofMover (class in pyrosetta.rosetta.protocols.matdes) SymDofMoverSampler (class in pyrosetta.rosetta.protocols.matdes) SymEnergyCutRotamerTrialsMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymFoldandDockMoveRbJumpMover (class in pyrosetta.rosetta.protocols.symmetric_docking) SymFoldandDockSlideTrialMover (class in pyrosetta.rosetta.protocols.symmetric_docking) symm_count() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) symm_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) symm_type() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) symmetric_components() (in module pyrosetta.rosetta.core.pose.symmetry) symmetric_fold_tree() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_gly_tables() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) symmetric_residue_subset() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_rotamer_trials() (in module pyrosetta.rosetta.core.pack) symmetric_secstruct() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_sequence() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) SymmetricAddMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane.symmetry) SymmetricalResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) SymmetricConformation (class in pyrosetta.rosetta.core.conformation.symmetry) SymmetricCycpepAlign (class in pyrosetta.rosetta.protocols.cyclic_peptide) SymmetricFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) SymmetricRMSMover (class in pyrosetta.rosetta.protocols.symmetry) SymmetricRotamerSet_ (class in pyrosetta.rosetta.core.pack.rotamer_set.symmetry) symmetrize_by_intersection() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) symmetrize_by_union() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) symmetrize_fold_tree() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) symmetrize_scorefunction() (in module pyrosetta.rosetta.core.scoring.symmetry) symmetrize_spans() (in module pyrosetta.rosetta.protocols.membrane.symmetry) symmetry_compliance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) symmetry_info() (in module pyrosetta.rosetta.core.pose.symmetry) Symmetry_Info() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) symmetry_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) SymMinimizeInterface() (in module pyrosetta.rosetta.protocols.protein_interface_design) SymMinimizerMap (class in pyrosetta.rosetta.core.optimization.symmetry) SymMinMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymPackRotamersMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymRotamerTrialsMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymUnsatHbondFilter (class in pyrosetta.rosetta.protocols.matdes) SYN_ANTI_RESTRICTION (class in pyrosetta.rosetta.core.fragment.rna) sync_objects_with_flags() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) sys_sleep() (in module pyrosetta.rosetta.utility)