Index – N

N() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) n() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) n_active_score_types() (pyrosetta.rosetta.core.scoring.EnergyGraph method) n_ang_U1D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_ang_U2D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_atom() (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) N_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) n_atomtypes() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) n_bonded_neighbor_all_res() (pyrosetta.rosetta.core.conformation.Residue method) n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) n_ca_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) n_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) n_ca_c_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) n_children() (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) n_columns() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) n_correctly_aligned_positions() (in module pyrosetta.rosetta.core.sequence) n_current_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) n_cycles() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) n_default_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) n_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager 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) n_designed() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) n_dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_elements() (pyrosetta.rosetta.core.chemical.ElementSet method) n_external_samplers() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) n_fragment_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_fragment_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_geometric_constraints() (pyrosetta.rosetta.protocols.match.Matcher method) n_hbond_acceptors() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_hbond_donors() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_helices() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) n_key() (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) n_loops() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) n_lower() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) n_mainchain_atoms() (pyrosetta.rosetta.core.conformation.Residue method) n_mutants() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) n_non_polymeric_residue_connections() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_nonchitip_atoms_for_chi() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) n_nonjump_children() (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) n_nus() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_omega() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) n_orbitals() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_parameters() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) n_parameters_sets() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) n_part() (pyrosetta.rosetta.utility.options.OptionCollection method) n_part_prefix_match() (pyrosetta.rosetta.utility.options.OptionCollection method) n_polymeric_residue_connections() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_possible_hits_per_upstream_conformation() (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) n_possible_residue_connections() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_property_sets() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) n_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) n_real_dofs() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) n_reference_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) n_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) n_residue_connections_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) n_residues() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) n_residues_after_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) n_residues_before_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) n_rings() (pyrosetta.rosetta.core.chemical.ResidueType method) n_rows() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) n_sample() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) n_samples_per_side_of_nrchi_bin() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) n_samples_wi_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) n_scores() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_segment() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) n_sequence_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) n_temp_levels() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) n_terminal_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) n_terminus_size() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) n_tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_torsion_sets() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) n_torsions() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) n_torsions_total() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) n_trees() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) n_types() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) n_unassigned() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) n_upper() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) n_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) n_virtual_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) na_analogue() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nali() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) name() (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter 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.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.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.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter 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.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover 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.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.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.EntityElement 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.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter 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.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.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.fragments.FullAtomRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.simple_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.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator 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.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName 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) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) name1() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) name2suite() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) name3() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) name3_from_oneletter() (in module pyrosetta.rosetta.protocols.motifs) name_for_common_type() (in module pyrosetta.rosetta.utility.tag) name_from_aa() (in module pyrosetta.rosetta.core.chemical) name_from_database_mode() (in module pyrosetta.rosetta.utility.sql_database) name_from_elements() (in module pyrosetta.rosetta.core.chemical.element) name_from_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) name_from_score_type() (in module pyrosetta.rosetta.core.scoring) name_from_transaction_mode() (in module pyrosetta.rosetta.utility.sql_database) name_map() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) name_mapOP() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) name_to_listener_tag() (in module pyrosetta.rosetta.basic.mpi) name_wo_rgstr() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) named_atom_id_to_atom_id() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) named_stub_id_to_stub_id() (in module pyrosetta.rosetta.core.pose) NamedAngleConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) NamedAtomID (class in pyrosetta.rosetta.core.id) NamedAtomPairConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) NamedSegmentSelector (class in pyrosetta.rosetta.protocols.denovo_design.residue_selectors) NamedStubID (class in pyrosetta.rosetta.core.id) nangles() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) NATAA (class in pyrosetta.rosetta.core.pack.task) NatbiasSecondaryStructureEnergy (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) NatbiasStrandPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) native_CA_gdtmm() (in module pyrosetta.rosetta.core.scoring) native_CA_rmsd() (in module pyrosetta.rosetta.core.scoring) native_distance_viol() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) native_edensity_score_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) native_loop_core_CA_rmsd() (in module pyrosetta.rosetta.protocols.loops) native_positions() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) native_secstruct() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) native_tag() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) NativeAntibodySeq (class in pyrosetta.rosetta.protocols.antibody.design) NativeEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) natives_select() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) natom() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) natom_aligned() (in module pyrosetta.rosetta.protocols.hybridization) natoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) NATRO (class in pyrosetta.rosetta.core.pack.task) nb_list() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) nbb() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) nblist_dis2_cutoff_HH() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nblist_dis2_cutoff_XH() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nblist_dis2_cutoff_XX() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nbonds() (pyrosetta.rosetta.core.chemical.ResidueType method) nbonds_from_bb_atom() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) nbr_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nbr_atom_rmsd() (in module pyrosetta.rosetta.core.scoring) nbr_atom_xyz() (pyrosetta.rosetta.core.conformation.Residue method) nbr_e_threshold() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) nbr_radius() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nbr_vertex() (pyrosetta.rosetta.core.chemical.ResidueType method) nbrs() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) NC (class in pyrosetta.rosetta.core.pack.task) NCAARotLibBBTorsions (class in pyrosetta.rosetta.core.chemical) NCAARotLibNumRotamerBins (class in pyrosetta.rosetta.core.chemical) NCAARotLibPath (class in pyrosetta.rosetta.core.chemical) NCaCaC_Dihedral_Func (class in pyrosetta.rosetta.core.scoring.disulfides) ncbb_design_main_loop() (in module pyrosetta.rosetta.protocols.ncbb) nchi() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ncluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) nContinuousSegments() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) NCSResMapping (class in pyrosetta.rosetta.protocols.simple_moves.symmetry) ncsts() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) ncycle() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) ndihe() (pyrosetta.rosetta.core.chemical.ResidueType method) ndims() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) nDoFs() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) nearby_atom_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) nearby_atom_cutoff() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) nearest_atom_for_constraint() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) nearest_neighbor() (in module pyrosetta.rosetta.numeric.kdtree) nearest_neighbors() (in module pyrosetta.rosetta.numeric.kdtree) nearest_ssize() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) neg_space_element_allocation_error_message() (in module pyrosetta.rosetta.utility.graph) negate() (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) neighbor_count() (in module pyrosetta.rosetta.protocols.sic_dock) neighbor_cutoff() (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) neighbor_detection_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) neighbor_dis() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) neighbor_hits() (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) neighbor_id() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) neighbor_min() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_min_add() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_min_clear() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_strands() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) NeighborDependentTabooSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) NeighborDependentTorsionSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) Neighborhood (class in pyrosetta.rosetta.protocols.neighbor) neighborhood_calc() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) NeighborhoodByDistanceCalculator (class in pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators) NeighborhoodResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) NeighborList (class in pyrosetta.rosetta.core.scoring) neighbors() (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) NeighborsByDistanceCalculator (class in pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators) Nend_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) Nend_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) netTargetPocketVolume() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) network_analysis() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) network_analysis2() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) network_anchoring() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) network_anchoring_per_residue() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) network_contains_aa() (in module pyrosetta.rosetta.protocols.hbnet) new_chain_order() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) new_chemical_bond() (pyrosetta.rosetta.core.kinematics.FoldTree method) new_decoy() (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) new_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) new_icoor() (pyrosetta.rosetta.core.chemical.Orbital method) new_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) new_omega() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) new_orbital_icoor_data() (pyrosetta.rosetta.core.chemical.ResidueType method) new_phi() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) new_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager 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) new_psi() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) new_secondary_structure_override() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) new_sequence_override() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) new_sfr() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) new_sym_min() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) newDataLoader() (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) newTopologyClaimer() (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) next() (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) next_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) next_child() (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) next_job() (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) next_resnum() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) next_segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) next_torsion_string() (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.TabooSamplingKinematicPerturber method) nfft() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) ngroups() (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) nhbonds() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) nheavyatoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nint() (in module pyrosetta.rosetta.ObjexxFCL) niter() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) nl_if() (in module pyrosetta.rosetta.ObjexxFCL.format) nlevels_per_dim() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) nloop() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) nmodes() (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) nmoltenres() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) nmoves() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) nmtr() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) NO_ADDUCTS (class in pyrosetta.rosetta.core.pack.task) no_chainend_ter() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) no_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) no_optH() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) no_output_cen() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) no_relax() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) NoClient (class in pyrosetta.rosetta.utility.keys) NoDefault() (pyrosetta.rosetta.utility.options.BooleanOption method)

nodes() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) NoesyModule (class in pyrosetta.rosetta.protocols.noesy_assign) NomenclatureManager (class in pyrosetta.rosetta.core.io) non_const_pose() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) non_helix_in_membrane_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) non_ideal() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) non_main_chain_sugar_coords() (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) non_main_chain_sugar_coords_defined() (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) non_peptide_heavy_atom_RMSD() (in module pyrosetta.rosetta.core.scoring) non_virtual_score() (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) nonadduct_variants_match() (in module pyrosetta.rosetta.core.chemical) noncanonical_atom_count() (in module pyrosetta.rosetta.core.pose) noncanonical_chi_count() (in module pyrosetta.rosetta.core.pose) noncanonical_residue_count() (in module pyrosetta.rosetta.core.pose) nonchitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) nonchitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) nonconst_atom() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_atom_numbers_for_mg_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_atom_numbers_for_vdw_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_atoms() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) nonconst_begin() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) nonconst_cenlist_from_pose() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) nonconst_circle() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) nonconst_data() (pyrosetta.rosetta.core.conformation.Residue method) nonconst_data_ptr() (pyrosetta.rosetta.core.conformation.Residue method) nonconst_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_direction() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_downstream_algorithms() (pyrosetta.rosetta.protocols.match.Matcher method) nonconst_end() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) nonconst_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) nonconst_generators() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_id() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_interface_from_pose() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) nonconst_is_buried() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_is_interface() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_is_magnesium() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_long_range_container() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) nonconst_Membrane_FAEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_MembraneEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_MembraneTopology_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_monopole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_mp_param() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_other_struct_list() (pyrosetta.rosetta.core.io.silent.SilentStruct method) nonconst_partners() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_power() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_quadrupole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rad() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_rad2() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_res() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) nonconst_resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) nonconst_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) nonconst_rKirkwood() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rna_scoring_info_from_pose() (in module pyrosetta.rosetta.core.scoring.rna) nonconst_rna_task() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) nonconst_rosetta_res_type() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rotamer() (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) nonconst_stored_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_stored_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) nonconst_vdw_type() (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) nonconst_xyz() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) NonContinuousFrame (class in pyrosetta.rosetta.core.fragment) nondefault() (pyrosetta.rosetta.core.chemical.ResidueType method) nonlocal_pairs() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) NonlocalFrags_main() (in module pyrosetta.rosetta.protocols.frag_picker.nonlocal) NonlocalPair (class in pyrosetta.rosetta.protocols.frag_picker.nonlocal) nonmatching_residues() (in module pyrosetta.rosetta.core.io.external) nonmonotone() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) nonnegative_principal_angle_degrees() (in module pyrosetta.rosetta.numeric) nonpivot_residues() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) NonResidueTypeConstraint (class in pyrosetta.rosetta.core.scoring.constraints) nonzero_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) nonzero_hbond_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) nooutput() (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) NoOutputJobOutputter (class in pyrosetta.rosetta.protocols.jd2) NoRepackDisulfides (class in pyrosetta.rosetta.core.pack.task.operation) norm() (in module pyrosetta.rosetta.numeric.kinematic_closure) norm_factor() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) norm_squared() (pyrosetta.rosetta.core.scoring.EMapVector method) normal() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) normal_to_ellipsoid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) normalize_to_thk() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) normalized_distance_in_degrees() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) normalized_peak_volume() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) NormalizedEvaluatedArchive (class in pyrosetta.rosetta.protocols.jd2.archive) normalizing_area() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total_hydrophobic_atoms_only() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total_polar_atoms_only() (in module pyrosetta.rosetta.core.scoring) NormalModeMinimizer (class in pyrosetta.rosetta.protocols.normalmode) NormalModeMultifunc (class in pyrosetta.rosetta.protocols.normalmode) not_already_connected() (in module pyrosetta.rosetta.protocols.dna) not_blank() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) not_empty() (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) not_end() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) not_unbounded() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) not_universal_main() (in module pyrosetta.rosetta.protocols.jobdist) not_using() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) not_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) NOTAA (class in pyrosetta.rosetta.core.pack.task) note_coordinate_change_registered() (pyrosetta.rosetta.core.kinematics.AtomTree method) note_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) note_long_range_interactions_exist_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_rpe_calculated() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_short_range_interactions_exist_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_submatrix_accessed() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_submatrix_added() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_vertex_reached() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) notify() (in module pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) notify_destructed() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) notify_energy_change() (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) notify_structure_change() (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) NotJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) NotResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) npd_hb_eval_type_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) npd_hb_weight() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) npd_hbond_set() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) NPDHBondEnergy (class in pyrosetta.rosetta.core.scoring.hbonds) NPDHBondSet (class in pyrosetta.rosetta.core.scoring.hbonds) NPDHBSimpleInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) NPDPropCalculator (class in pyrosetta.rosetta.protocols.pack_daemon) nr_frags() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) nr_frames() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) nr_moves() (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) nr_open_slaves() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) nr_res_affected() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) nr_residues() (pyrosetta.rosetta.protocols.loops.Loops method) NRbisafe() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) nrchi_prob_minimum_for_extra_samples() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) nread_limit_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) nreads_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) nres() (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.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) nres_protein() (in module pyrosetta.rosetta.core.pose) nrot() (pyrosetta.rosetta.protocols.mean_field.AAProb method) nsol() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) nstrand_values() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) nstruct() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) nstruct_centroid() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) nstruct_index() (pyrosetta.rosetta.protocols.jd2.Job method) nstruct_max() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) nterm_included() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) ntrials() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) ntries() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) nu() (pyrosetta.rosetta.core.conformation.Residue method) nu1_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu1_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu2_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu2_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) NucleotideMutation (class in pyrosetta.rosetta.protocols.evolution) NullPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) NullPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) NullResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) NullResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) NullStream (class in pyrosetta.rosetta.basic.resource_manager.locator) num_accepted_scores() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) num_accepts() (pyrosetta.rosetta.protocols.moves.TrialMover method) num_atoms() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) num_bins() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) num_bondangles() (pyrosetta.rosetta.core.chemical.ResidueType method) num_bulge() (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepSequence method) num_chains() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.frags.VallData method) num_chi_angles() (in module pyrosetta.rosetta.core.pose) num_chunk_sets() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) num_chunks() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) num_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) num_designable() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) num_dimensions() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) num_domains() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) num_edges() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) num_elements() (pyrosetta.rosetta.utility.recent_history_queue method) num_fragpick() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) num_geom_cst() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) num_hbond_acceptors() (in module pyrosetta.rosetta.core.pose) num_hbond_donors() (in module pyrosetta.rosetta.core.pose) num_heavy_atoms() (in module pyrosetta.rosetta.core.pose) num_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) num_lines_in_file() (in module pyrosetta.rosetta.protocols.cluster.calibur) num_loop() (pyrosetta.rosetta.protocols.loops.Loops method) num_loops() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) num_mcfis() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) num_moving_chunks() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) num_negative_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) num_neighbors() (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) num_neighbors_counting_self() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) num_neighbors_counting_self_static() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) num_nodes() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) num_packed() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) num_pairings() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) num_pose_minimize() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) num_poses() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) num_positions() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) num_positive_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) num_pts() (pyrosetta.rosetta.protocols.cluster.APCluster method) num_random_samples() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) num_rejections() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) num_residues() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) num_rings() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) num_rotamers() (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.optimize_weights.OptEData method) num_segments() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) num_selectors() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) num_seqpos_lists() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) num_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) num_steps() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) num_strands() (in module pyrosetta.rosetta.protocols.denovo_design.components) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) num_strings() (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.TabooSamplingKinematicPerturber method) num_target_states() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) num_to_be_packed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) num_trials() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) num_triggers() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) number() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) number_bonded_heavyatoms() (pyrosetta.rosetta.core.chemical.ResidueType method) number_bonded_hydrogens() (pyrosetta.rosetta.core.chemical.ResidueType method) number_heavy_chain() (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) number_light_chain() (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) number_of_atoms() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) number_of_high_resolution_cycles() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) number_of_residues() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) Numberer (class in pyrosetta.rosetta.protocols.antibody.grafting) numbering_scheme() (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) numbering_scheme_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numbering_scheme_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numbering_scheme_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numchanges() (in module pyrosetta.rosetta.numeric.kinematic_closure) numeric_properties() (pyrosetta.rosetta.core.chemical.ResidueProperties method) numerical_derivative_check() (in module pyrosetta.rosetta.core.optimization) (in module pyrosetta.rosetta.core.optimization.symmetry) numGaussians() (pyrosetta.rosetta.core.scoring.func.USOGFunc method) NumNeighborsMPM (class in pyrosetta.rosetta.protocols.match) numpy_to_rosetta() (in module pyrosetta.toolbox.numpy_utils) numroots() (in module pyrosetta.rosetta.numeric.kinematic_closure) nus() (pyrosetta.rosetta.core.conformation.Residue method) nusing() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) nvar() (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method)