Index – I

I() (in module pyrosetta.rosetta.ObjexxFCL.format) i() (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) i2() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) i3() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) i_next() (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) IACHAR() (in module pyrosetta.rosetta.ObjexxFCL) ICHAR() (in module pyrosetta.rosetta.ObjexxFCL) iCode() (pyrosetta.rosetta.core.io.ResidueInformation method) icode() (pyrosetta.rosetta.core.pose.PDBInfo method) icoor() (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) ICoorAtomID (class in pyrosetta.rosetta.core.chemical) ICoorAtomID.Type (class in pyrosetta.rosetta.core.chemical) icstream (class in pyrosetta.rosetta.utility.io) id() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) id_for_current_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) idate() (in module pyrosetta.rosetta.ObjexxFCL) idCode() (pyrosetta.rosetta.core.io.HeaderInformation method) ideal_bond_length_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) ideal_score() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) ideal_val() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) ideal_xyz() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.Orbital method) IdealAbegoGenerator (class in pyrosetta.rosetta.protocols.denovo_design.components) IdealBondLengthSet (class in pyrosetta.rosetta.core.chemical) idealize_combined_pose() (in module pyrosetta.rosetta.protocols.grafting) idealize_hydrogens() (in module pyrosetta.rosetta.core.conformation) idealize_insert() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) idealize_last_n_glycans_in_pose() (in module pyrosetta.rosetta.core.pose.carbohydrates) idealize_loop() (in module pyrosetta.rosetta.protocols.loops) idealize_position() (in module pyrosetta.rosetta.core.conformation) idealize_proline_nvs() (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) idealize_sidechains() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) IdealizeMover (class in pyrosetta.rosetta.protocols.idealize) IdealizeNonPhiPsi (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) IdealParameters (class in pyrosetta.rosetta.protocols.kinematic_closure) IdealParametersDatabase (class in pyrosetta.rosetta.core.scoring.methods) identical_info_consistency_check() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) identifier() (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) identify_and_set_cdr_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) identify_hbonds_1way() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_hbonds_1way_AHdist() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_hbonds_1way_membrane() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_intra_res_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_sheet_id_by_residue_end() (in module pyrosetta.rosetta.protocols.features.strand_assembly) identities() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) identity() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) identity_transform() (pyrosetta.rosetta.core.kinematics.Jump method) IdentityEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) IdentityEvent (class in pyrosetta.rosetta.core.conformation.signals) IdentityEvent.Tag (class in pyrosetta.rosetta.core.conformation.signals) idle() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) if_late_scoring_for_zeros() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) ifft3() (in module pyrosetta.rosetta.numeric.fourier) ifft3_dynamic() (in module pyrosetta.rosetta.numeric.fourier) IfThenFilter (class in pyrosetta.rosetta.protocols.filters) ig() (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) IGEdgeReweightContainer (class in pyrosetta.rosetta.core.pack.task) IGEdgeReweighter (class in pyrosetta.rosetta.core.pack.task) IGEdgeReweights() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) ignore() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) ignore_cmdline_enzdes_cstfile() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) ignore_default_task() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) ignore_light_chain() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) ignore_residues_in_csts() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) ignore_sugars() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ignore_unconnected_upper() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) ignore_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ignore_waters() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ignore_zero_occupancy() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ignored() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) ignorefinished() (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) import() (pyrosetta.rosetta.core.kinematics.MoveMap method) import_false() (pyrosetta.rosetta.core.kinematics.MoveMap method) import_pose_from_silent_file() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) import_true() (pyrosetta.rosetta.core.kinematics.MoveMap method) ImportPoseOptions (class in pyrosetta.rosetta.core.import_pose) impose_constraints() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) improper_dihedral() (pyrosetta.rosetta.core.chemical.ResidueType method) improper_dihedrals_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) in_a_submotif() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) in_a_submotif_seed() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) in_blacklist() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) in_charge() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) in_membrane() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) in_ngbat_sphere() (in module pyrosetta.rosetta.protocols.neighbor) in_nrg_graph() (in module pyrosetta.rosetta.protocols.neighbor) in_paired_strands() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) include_current() (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) include_gly() (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) include_lips() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) include_native_aa() (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) include_native_restype() (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) include_neighbors() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) include_only_center_clusters() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_current_cluster() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_germlines() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_germlines_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_germlines_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_resid() (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) include_residue() (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) include_trp() (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) include_virtual_side_chain() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) incomplete() (pyrosetta.rosetta.core.chemical.ResConnID method) increase_multi_cool_annealer_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) increase_packer_residue_radius() (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) increasing() (pyrosetta.rosetta.protocols.loops.Loop method) increment_both() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_both_and_cache() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_client_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) increment_cur_indices() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) increment_edge_list_iterator() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) increment_from_cached() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_hbond_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) increment_npd_hbond_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) increment_nread_limit() (pyrosetta.rosetta.utility.io.FileContentsMap method) increment_reference_pose_mapping_after_seqpos() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) increment_self_overlap() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_this_and_cache() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) indel_motif() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) indel_motif_radius() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) indel_motif_seq_id() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) indent_w_spaces() (in module pyrosetta.rosetta.utility.tag) independent_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) IndependentBBTorsionSRFD (class in pyrosetta.rosetta.core.fragment) index() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) index2symbol() (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.SSManager method) index2symbolString() (pyrosetta.rosetta.core.sequence.SSManager method) IndexRange (class in pyrosetta.rosetta.ObjexxFCL) indicate_required_context_graphs() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) info() (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) inherit_scorefxn_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) ini_func1() (in module pyrosetta.rosetta.numeric.random) ini_func2() (in module pyrosetta.rosetta.numeric.random) init() (in module pyrosetta) (in module pyrosetta.rosetta.basic) (in module pyrosetta.rosetta.core.init) (in module pyrosetta.rosetta.protocols.init) (pyrosetta.rosetta.basic.Tracer method) Init() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) init() (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover 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.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) init_angle() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) init_bbgmover() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) init_beta_correction() (in module pyrosetta.rosetta.core.init) init_beta_july15_correction() (in module pyrosetta.rosetta.core.init) init_beta_nov16_correction() (in module pyrosetta.rosetta.core.init) init_common_options() (in module pyrosetta.rosetta.protocols.ncbb) init_correct_correction() (in module pyrosetta.rosetta.core.init) init_crystal_refinement_correction() (in module pyrosetta.rosetta.core.init) init_cst_score_types() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) init_disp() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) init_dna_correction() (in module pyrosetta.rosetta.core.init) init_facts_correction() (in module pyrosetta.rosetta.core.init) init_from_cmd() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) init_from_comand_line() (pyrosetta.rosetta.core.pack.task.operation.OptH method) init_from_decoy_set() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) init_from_file() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) init_from_lines() (pyrosetta.rosetta.core.io.silent.SilentStruct method) init_from_options() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) init_from_pose() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) init_from_vector() (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) init_hbond_sp2_correction() (in module pyrosetta.rosetta.core.init) init_kic_loop() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) init_membrane_center_normal() (pyrosetta.rosetta.core.scoring.MembranePotential method) init_nonideal_correction() (in module pyrosetta.rosetta.core.init) init_on_new_input() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) init_option() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) init_packing_score_discrim() (in module pyrosetta.rosetta.core.scoring.packstat) init_packing_score_respred() (in module pyrosetta.rosetta.core.scoring.packstat) init_paths() (in module pyrosetta.rosetta.core.init) init_profiling() (in module pyrosetta.rosetta.core.init) init_random_generators() (in module pyrosetta.rosetta.core.init) init_random_number_generators() (in module pyrosetta.rosetta.core.init) init_resources() (in module pyrosetta.rosetta.core.init) init_restore_score12prime() (in module pyrosetta.rosetta.core.init) init_revert_to_pre_talaris_2013_mistake() (in module pyrosetta.rosetta.core.init) init_revert_to_talaris() (in module pyrosetta.rosetta.core.init) init_rotamers_centroids() (in module pyrosetta.rosetta.protocols.make_rot_lib) init_score_function_corrections() (in module pyrosetta.rosetta.core.init) init_sequence() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) init_shapovalov_lib_fixes_enable_correction() (in module pyrosetta.rosetta.core.init) init_source_revision() (in module pyrosetta.rosetta.core.init) init_spades_score_function_correction() (in module pyrosetta.rosetta.core.init) init_task() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) init_tracers() (in module pyrosetta.rosetta.core.init) init_with_options() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) initialize() (in module pyrosetta.rosetta.basic.options) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 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.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) initialize_and_check() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) initialize_atomid_map() (in module pyrosetta.rosetta.core.pose) initialize_atomid_map_AtomID() (in module pyrosetta.rosetta.core.pose) initialize_atoms_for_which_we_need_new_dofs() (in module pyrosetta.rosetta.core.pose.rna) initialize_betaresidue_minima() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) initialize_disulfide_bonds() (in module pyrosetta.rosetta.core.pose) initialize_dofs() (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) initialize_dun02_aa_parameters() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) initialize_extra_rotamer_flags_from_command_line() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) initialize_extra_rotamer_flags_from_options() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) initialize_filter() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) initialize_for_de_novo_protocol() (pyrosetta.rosetta.protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer method) initialize_from() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) initialize_from_command_line() (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) initialize_from_file() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.protocols.match.Matcher method) initialize_from_file_contents() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) initialize_from_file_contents_and_check() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) initialize_from_matcher_task() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) initialize_from_options() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) initialize_from_params() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) initialize_from_residue_type() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) initialize_from_task() (pyrosetta.rosetta.protocols.match.Matcher method) initialize_from_tokens() (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.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) initialize_ga_randomizer_from_entity_task() (in module pyrosetta.rosetta.protocols.pack_daemon) initialize_HBEval_lookup() (in module pyrosetta.rosetta.core.scoring.hbonds) initialize_hbs() (in module pyrosetta.rosetta.core.pose.ncbb) initialize_input_streams() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) initialize_input_streams_with_residue_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) initialize_jump_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_logging() (in module pyrosetta.logging_support) initialize_native_and_align_pose() (in module pyrosetta.rosetta.protocols.stepwise.setup) initialize_ncbbs() (in module pyrosetta.rosetta.core.pose.ncbb) initialize_o2prime_pack_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_oops() (in module pyrosetta.rosetta.core.pose.ncbb) initialize_pack_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_parameters() (in module pyrosetta.rosetta.core.pose.full_model_info) initialize_pose_and_other_poses_from_command_line() (in module pyrosetta.rosetta.core.import_pose) initialize_pose_and_other_poses_from_options() (in module pyrosetta.rosetta.core.import_pose) initialize_pose_for_rotset_creation() (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) initialize_random_chunks() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) initialize_residue_map_from_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) initialize_residue_type() (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) initialize_rna_chunk_library() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) initialize_rnp_aa_rna_backbone() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_rnp_base_pair() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_rnp_pair() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_sample_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_samples() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) initialize_simulation() (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.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver 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.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.utility.SimulateMPI method) initialize_ss() (in module pyrosetta.rosetta.protocols.comparative_modeling) initialize_stub() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) initialize_sturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) initialize_tag_is_done() (in module pyrosetta.rosetta.core.io.silent) initialize_task_from_entity_resfile_and_secondary_resfile() (in module pyrosetta.rosetta.protocols.pack_daemon) initialize_thermal_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_tree_nodes_from_enzcst_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) initialize_weights() (pyrosetta.rosetta.protocols.moves.TrialMover method) initialize_xyz_parameters() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) InitializeByBins (class in pyrosetta.rosetta.protocols.simple_moves.bin_transitions) initialized() (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) InitializeFromOptionCollection (class in pyrosetta.rosetta.core.pack.task.operation) InitializerSentinel (class in pyrosetta.rosetta.ObjexxFCL.internal) inner_job() (pyrosetta.rosetta.protocols.jd2.Job method) inner_job_nonconst() (pyrosetta.rosetta.protocols.jd2.Job method) InnerJob (class in pyrosetta.rosetta.protocols.jd2) inplace_product() (in module pyrosetta.rosetta.numeric) inplace_transpose_product() (in module pyrosetta.rosetta.numeric) inprogress() (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) input_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) input_etable() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) input_legrand_sasa_dats() (in module pyrosetta.rosetta.core.scoring.sasa) input_pdb_files_from_command_line() (in module pyrosetta.rosetta.protocols.jd2) input_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) input_sasa_dats() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.core.scoring.packstat.old) input_set() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_defined() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_selector() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_selector_defined() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_string() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_source() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) input_stub_atom0() (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) input_stub_atom0_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom1() (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) input_stub_atom1_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom2() (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) input_stub_atom2_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom3() (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) input_stub_atom3_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_tag() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) InputStreamWithResidueInfo (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) insert() (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.sewing.Hasher method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) insert_aligned_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_aligned_residue_safe() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_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) insert_cdr_into_antibody() (in module pyrosetta.rosetta.protocols.antibody.design) insert_chain_ending() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) insert_chunk_into_pose() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) insert_conformation_by_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) insert_connected_segment() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) insert_connection_scheme() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_dssp_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_edge_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_fold_tree_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_fragment() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) insert_hit() (pyrosetta.rosetta.protocols.match.HitHasher method) insert_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) insert_ideal_bonds_at_polymer_junction() (in module pyrosetta.rosetta.core.conformation) insert_ideal_geometry_at_polymer_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) insert_ideal_geometry_at_residue_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) insert_ideal_mainchain_bonds() (in module pyrosetta.rosetta.core.conformation) insert_map() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) insert_match_into_pose() (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) insert_observer() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) insert_or_ignore() (in module pyrosetta.rosetta.basic.database) insert_peptide_edges() (in module pyrosetta.rosetta.protocols.denovo_design) insert_polymer_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_pose() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_pose_into_pose() (in module pyrosetta.rosetta.protocols.grafting) insert_pose_torsion_override_movemap() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_position() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) insert_random_fragments_in_flexible_protein_regions() (in module pyrosetta.rosetta.protocols.frags) insert_random_protein_chunks() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) insert_residue_by_bond() (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) insert_residue_by_chemical_bond() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_residue_by_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.Pose method) insert_residue_into_atom_tree() (in module pyrosetta.rosetta.core.conformation) insert_sampled_torsion_string_into_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) insert_score_function_method_options_rows() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) insert_size() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) insert_source_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_ss_into_pose_no_IG_helix() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_target_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insertion_char() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertion_code() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) insertion_end_residue() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertion_length() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) insertion_order() (pyrosetta.rosetta.basic.resource_manager.JobOptions method) insertion_point_absolute_index() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertion_start_residue() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) InsertPoseIntoPoseMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) InSetExpression (class in pyrosetta.rosetta.protocols.pack_daemon) inside_boundaries() (in module pyrosetta.rosetta.core.membrane) instance() (pyrosetta.rosetta.protocols.checkpoint.Timer method) instantiate_any_virtual_sugars() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) instantiate_water_at_octahedral_vertex() (in module pyrosetta.rosetta.protocols.magnesium) instantiated_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) int2afteroption() (in module pyrosetta.rosetta.basic.options) int_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) int_to_orientation() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) intafteroption() (in module pyrosetta.rosetta.basic.options) integer() (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) integer_range_restriction() (in module pyrosetta.rosetta.utility.tag) IntegerOption (class in pyrosetta.rosetta.utility.options) IntegerOptionKey (class in pyrosetta.rosetta.utility.options) IntegerVectorOption (class in pyrosetta.rosetta.utility.options) IntegerVectorOptionKey (class in pyrosetta.rosetta.utility.options) integration_test_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) intensity() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) inter() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) inter_residue_connection_partner() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) InteractingRotamerExplosion (class in pyrosetta.rosetta.protocols.toolbox.task_operations) InterbondAngleScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) InterchainJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) InterchainPotential (class in pyrosetta.rosetta.protocols.scoring)

interchangeability_group() (pyrosetta.rosetta.core.chemical.ResidueType method) Interface (class in pyrosetta.rosetta.protocols.ligand_docking.ligand_options) interface() (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) interface_builder_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) interface_calc() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) interface_detection_dis() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) interface_distance_cutoff() (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) interface_from_pose() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) interface_nres() (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) InterfaceAnalyzerMover (class in pyrosetta.rosetta.protocols.analysis) InterfaceBuilderLoader (class in pyrosetta.rosetta.protocols.ligand_docking) InterfaceData (class in pyrosetta.rosetta.protocols.analysis) InterfaceDdGMover (class in pyrosetta.rosetta.protocols.features) InterfaceFeatures (class in pyrosetta.rosetta.protocols.features) InterfaceFeaturesCreator (class in pyrosetta.rosetta.protocols.features) InterfaceInfo (class in pyrosetta.rosetta.protocols.ligand_docking.ligand_options) (class in pyrosetta.rosetta.protocols.scoring) InterfaceRecapitulationMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) InterGroupInterfaceByVectorSelector (class in pyrosetta.rosetta.core.select.residue_selector) InterGroupNeighborsCalculator (class in pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators) InterlockAroma (class in pyrosetta.rosetta.protocols.flxbb) intermediate_structs() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) interp_dspline() (in module pyrosetta.rosetta.core.scoring.electron_density) interp_spline() (in module pyrosetta.rosetta.core.scoring.electron_density) interpolate_2d_func_of_angles() (in module pyrosetta.rosetta.basic) interpolate_bilinear() (in module pyrosetta.rosetta.basic) interpolate_bilinear_by_value() (in module pyrosetta.rosetta.basic) interpolate_get_angle_bins() (in module pyrosetta.rosetta.basic) interpolate_polylinear_by_value() (in module pyrosetta.rosetta.core.pack.dunbrack) interpolate_trilinear() (in module pyrosetta.rosetta.basic) interpolate_trilinear_by_value() (in module pyrosetta.rosetta.basic) interpolate_value_and_deriv() (in module pyrosetta.rosetta.core.scoring) interpolated_analytic_etable_evaluation() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) interpolation_type_enum_to_string() (in module pyrosetta.rosetta.protocols.canonical_sampling) interpolation_type_string_to_enum() (in module pyrosetta.rosetta.protocols.canonical_sampling) intersect() (in module pyrosetta.rosetta.core.membrane) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) intersect_nic() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) intersects() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.forge.build.Interval method) Interval (class in pyrosetta.rosetta.protocols.forge.build) (class in pyrosetta.rosetta.protocols.jumping) interval() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) interval_to_loop() (in module pyrosetta.rosetta.protocols.forge.methods) intra_elec_scale() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) intra_solv_scale() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) intracomponent_contact() (in module pyrosetta.rosetta.core.pose.symmetry) intrares_upper_atom_neighbors() (pyrosetta.rosetta.core.scoring.NeighborList method) ints_of() (in module pyrosetta.rosetta.ObjexxFCL) inv_virtual_type_for_conf() (in module pyrosetta.rosetta.core.conformation) invalidate() (pyrosetta.rosetta.utility.signals.Link method) invalidate_residues_spanning_cuts() (in module pyrosetta.rosetta.protocols.medal) invDcnst() (pyrosetta.rosetta.core.scoring.RDC_Rohl method) inverse() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) inverse_rotamers_against_residue() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) inverse_rt6() (in module pyrosetta.rosetta.core.scoring.motif) InverseRotamersRCG (class in pyrosetta.rosetta.protocols.forge.constraints) invert() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) invert_exclude_residues() (in module pyrosetta.rosetta.core.scoring) invert_helix() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) invert_include_residues() (in module pyrosetta.rosetta.protocols.evaluation) InvGeometricFunc (class in pyrosetta.rosetta.protocols.moves) involved_in_phosphate_torsion() (in module pyrosetta.rosetta.protocols.rna.denovo) InvRotamerDots (class in pyrosetta.rosetta.core.pack.interaction_graph) InvrotCollector (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) invrots() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) InvrotTarget (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTree (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTreeNodeBase (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTreeRCG (class in pyrosetta.rosetta.protocols.forge.constraints) invstub() (in module pyrosetta.rosetta.protocols.sic_dock) inward_normal_to_plane() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) irstream (class in pyrosetta.rosetta.utility.io) is_a_finitenumber() (in module pyrosetta.rosetta.numeric) is_a_submotif() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) is_a_submotif_seed() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) is_aa_name_unknown() (in module pyrosetta.rosetta.core.chemical) is_acceptor() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) is_acetylated_nterminus() (pyrosetta.rosetta.core.chemical.ResidueType method) is_achiral_backbone() (pyrosetta.rosetta.core.chemical.ResidueType method) is_adduct() (pyrosetta.rosetta.core.chemical.ResidueType method) is_alpha_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_any_of() (in module pyrosetta.rosetta.ObjexxFCL) is_apolar() (pyrosetta.rosetta.core.conformation.Residue method) is_applicable() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) is_archive_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) is_aromatic() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_atom_axial_or_equatorial_to_ring() (in module pyrosetta.rosetta.core.chemical.rings) (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) is_atom_bin_in_range() (in module pyrosetta.rosetta.core.pose.rna) is_attached() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) is_backbone() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) is_base_phosphate_atom_pair() (in module pyrosetta.rosetta.core.chemical.rna) is_base_type() (pyrosetta.rosetta.core.chemical.ResidueType method) is_been_accessed() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) is_being_set() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) is_beta_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_beta_aminoacid() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) is_blank() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_blank_seq() (in module pyrosetta.rosetta.protocols.rna.movers) is_blank_string() (in module pyrosetta.rosetta.ObjexxFCL.format) is_bonded() (pyrosetta.rosetta.core.conformation.Residue method) is_bool() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_branch_point() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_bulge() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) is_buried() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) is_camelid() (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) is_cancelled() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) is_canonical() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) (pyrosetta.rosetta.core.chemical.ResidueType method) is_canonical_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_canonical_beta3_aa() (in module pyrosetta.rosetta.core.chemical) is_canonical_D_aa() (in module pyrosetta.rosetta.core.chemical) is_canonical_L_aa() (in module pyrosetta.rosetta.core.chemical) is_canonical_nucleic() (pyrosetta.rosetta.core.chemical.ResidueType method) is_carbohydrate() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_catalytic_seqpos() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) is_centroid() (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) is_changed() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) is_char() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_charged() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_chargedH() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) is_chemical_bond() (pyrosetta.rosetta.core.kinematics.Edge method) is_cl_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) is_close_chain_break() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) is_coarse() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_collinear() (in module pyrosetta.rosetta.core.kinematics.tree) is_compatible() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) is_compliant() (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) is_conjugatable() (pyrosetta.rosetta.core.chemical.Element method) is_conjugated() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) is_connect() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_connected() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) is_conserved() (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) is_continuous() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) is_copy() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) is_covalent() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) is_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_cutpoint_closed() (in module pyrosetta.rosetta.protocols.stepwise.modeler) is_cutpoint_closed_atom() (in module pyrosetta.rosetta.core.pose.rna) is_cutpoint_closed_torsion() (in module pyrosetta.rosetta.core.pose.rna) is_cutpoint_open() (in module pyrosetta.rosetta.core.pose.rna) is_cyclic() (pyrosetta.rosetta.core.chemical.ResidueType method) is_d_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_d_rna() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_designed() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) is_directory() (in module pyrosetta.rosetta.utility.file) is_disulfide() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) is_disulfide_bond() (in module pyrosetta.rosetta.core.conformation) is_disulfide_bonded() (pyrosetta.rosetta.core.chemical.ResidueType method) is_DNA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_donor() (pyrosetta.rosetta.core.chemical.AtomType method) is_double() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_empty() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) is_end_element() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) is_equivalent() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_experimental_technique() (pyrosetta.rosetta.core.io.HeaderInformation method) is_extended() (pyrosetta.rosetta.protocols.loops.Loop method) is_fake() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.Element method) is_false_string() (in module pyrosetta.rosetta.utility) is_float() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_flushed() (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Tracer method) is_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) is_freedof() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) is_fullatom() (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.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.fragments.FullAtomRNA_Fragments method) is_gamma_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_gasteiger_atom_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) is_geometry_initialized() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) is_glycosidic_omega2_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_omega_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_phi_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_psi_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) is_group() (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) is_h2o() (pyrosetta.rosetta.core.chemical.AtomType method) is_H3_rama_kinked() (in module pyrosetta.rosetta.protocols.antibody) is_haro() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) is_heavyatom() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.chemical.AtomType method) is_het() (pyrosetta.rosetta.core.pose.PDBInfo method) is_hydrogen() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) is_ideal_pose() (in module pyrosetta.rosetta.core.pose) is_ideal_position() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) is_identity() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) is_identity_ignore_gaps() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) is_in_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) is_in_list() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) is_in_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) is_inside() (in module pyrosetta.rosetta.protocols.hydrate) is_int() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_interface() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) is_interface_vector() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) is_internal() (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_ints() (in module pyrosetta.rosetta.ObjexxFCL) is_inverted_virtual_residue() (pyrosetta.rosetta.core.chemical.ResidueType method) is_jump() (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) is_jump_point() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_known_atom() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) is_l_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_l_rna() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_ladder() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) is_legal_greater_than() (in module pyrosetta.rosetta.numeric.kdtree) is_legal_kdtree_below_node() (in module pyrosetta.rosetta.numeric.kdtree) is_legal_less_than() (in module pyrosetta.rosetta.numeric.kdtree) is_ligand() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_ligand_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_ligand_heavyatom_residues() (in module pyrosetta.rosetta.core.scoring) is_lipid() (pyrosetta.rosetta.core.chemical.ResidueType method) is_literal() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) is_long() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_longdouble() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_loop() (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) is_loop_residue() (pyrosetta.rosetta.protocols.loops.Loops method) is_lower_cutpoint() (in module pyrosetta.rosetta.core.scoring.methods) is_lower_terminus() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_magnesium() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) is_mainchain_torsion_also_ring_torsion() (in module pyrosetta.rosetta.core.chemical) is_membrane() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) is_membrane_fixed() (in module pyrosetta.rosetta.protocols.membrane) is_membrane_moveable_by_itself() (in module pyrosetta.rosetta.protocols.membrane) is_mergeable() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) is_metal() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.NomenclatureManager method) is_metalbinding() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_methylated_cterminus() (pyrosetta.rosetta.core.chemical.ResidueType method) is_mirror_symmetric() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) is_mixed_mode() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) is_movable() (pyrosetta.rosetta.protocols.nonlocal.Chunk method) is_multi_trial() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) is_multicomponent() (in module pyrosetta.rosetta.core.pose.symmetry) is_n_methylated() (pyrosetta.rosetta.core.chemical.ResidueType method) is_NA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.NomenclatureManager method) is_nbr_atom() (in module pyrosetta.rosetta.core.scoring) is_non_peptide_heavy_atom() (in module pyrosetta.rosetta.core.scoring) is_nonempty_input_silent_file() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) is_nonpivot_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) is_normalization_enabled() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) is_num_in_list() (in module pyrosetta.rosetta.protocols.rna.denovo) is_observing() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.PDBInfo method) is_old_DNA() (pyrosetta.rosetta.core.io.NomenclatureManager method) is_old_RNA() (pyrosetta.rosetta.core.io.NomenclatureManager method) is_oligourea() (pyrosetta.rosetta.core.chemical.ResidueType method) is_on() (pyrosetta.rosetta.protocols.checkpoint.Timer method) is_original_type() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) is_orthogonal() (pyrosetta.rosetta.core.kinematics.Stub method) is_orthonormal() (in module pyrosetta.rosetta.core.scoring.dna) is_pair() (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) is_peptide() (pyrosetta.rosetta.core.kinematics.Edge method) is_peptoid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_perturbable() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) is_phosphate() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_pivot_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) is_polar() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_polar_hydrogen() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) is_polymer() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.kinematics.Edge method) is_polymer_bonded() (pyrosetta.rosetta.core.conformation.Residue method) is_polymer_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_polymer_lower() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_polymer_upper() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_position_conserved_residue() (in module pyrosetta.rosetta.core.pose) is_protected() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) is_protein() (in module pyrosetta.rosetta.protocols.stepwise.modeler) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_protein_backbone() (in module pyrosetta.rosetta.core.scoring) is_protein_backbone_including_O() (in module pyrosetta.rosetta.core.scoring) is_protein_CA() (in module pyrosetta.rosetta.core.scoring) is_protein_CA_or_CB() (in module pyrosetta.rosetta.core.scoring) is_protein_CA_or_equiv() (in module pyrosetta.rosetta.core.scoring) is_protein_sidechain_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_proton() (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) is_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) is_pseudo_bonded() (pyrosetta.rosetta.core.conformation.Residue method) is_purine() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pyrimidine() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_qsar_map_attached() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) is_referencepose_number() (in module pyrosetta.rosetta.core.pose) is_relevant() (pyrosetta.rosetta.utility.options.OptionCollection method) is_repulsive() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_required() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) is_res_exposed() (in module pyrosetta.rosetta.core.scoring.sasa) is_residues_in_contact() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) is_ring_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) is_RNA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_RNA_base() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_RNA_base_atom() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_rna_chainbreak() (in module pyrosetta.rosetta.core.pose.rna) is_root() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_rot_sample_name() (in module pyrosetta.rosetta.core.pack.task) is_same_sugar_pucker() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) is_scatom() (in module pyrosetta.rosetta.core.scoring) is_scofx_cstfied() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) is_set_s_kk() (pyrosetta.rosetta.protocols.cluster.DataPoint method) is_short() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_sidechain_amine() (pyrosetta.rosetta.core.chemical.ResidueType method) is_sidechain_thiol() (pyrosetta.rosetta.core.chemical.ResidueType method) is_similar_aa() (pyrosetta.rosetta.core.conformation.Residue method) is_similar_rotamer() (pyrosetta.rosetta.core.conformation.Residue method) is_simple_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_singlecomponent() (in module pyrosetta.rosetta.core.pose.symmetry) is_solution_trivial() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) is_solvent() (pyrosetta.rosetta.core.chemical.ResidueType method) is_sp2_proton_chi() (in module pyrosetta.rosetta.core.chemical) is_sparis_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) is_sri() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_string() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_string_numeric() (in module pyrosetta.rosetta.utility) is_sugar() (pyrosetta.rosetta.core.io.NomenclatureManager method) is_sugar_virtual() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) is_surface() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_symmetric() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) is_symmetric_partner_of() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) is_terminal() (pyrosetta.rosetta.protocols.loops.Loop method) is_terminus() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_this_strand_at_edge() (in module pyrosetta.rosetta.protocols.features.strand_assembly) is_this_strand_at_edge_by_looking_db() (in module pyrosetta.rosetta.protocols.features.strand_assembly) is_torsion_valid() (in module pyrosetta.rosetta.core.pose.rna) is_triazolemer() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_true_string() (in module pyrosetta.rosetta.utility) is_type() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_uint() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_ulong() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_undefined() (in module pyrosetta.rosetta.utility) is_upper_cutpoint() (in module pyrosetta.rosetta.core.scoring.methods) is_upper_terminus() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_ushort() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_using() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) is_valid() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) is_valid_chunk() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) is_valid_modification_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) is_valid_quota_pool_name() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) is_valid_record_type() (pyrosetta.rosetta.core.io.pdb.RecordCollection method) is_valid_ring_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) is_valid_sugar_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) is_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) is_variant_type() (pyrosetta.rosetta.core.chemical.ResidueProperties method) is_virtual() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.conformation.Residue method) is_virtual_base() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) is_virtual_residue() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) IsBondInRing() (pyrosetta.rosetta.core.chemical.Bond method) IsBondOrderKnown() (pyrosetta.rosetta.core.chemical.Bond method) isClose() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) isCompound() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isDigit() (in module pyrosetta.rosetta.protocols.sparta) isDirExists() (in module pyrosetta.rosetta.protocols.sparta) isEmpty() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isGenericRB() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isHelix() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isinf() (in module pyrosetta.rosetta.utility) isnan() (in module pyrosetta.rosetta.utility) isometry() (pyrosetta.rosetta.core.chemical.Bond method) isPowerOfTwo() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) isSheet() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isSimple() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isSolventExposed() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) isSpace() (in module pyrosetta.rosetta.protocols.sparta) isTarget() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) isTooSmall() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) iterate_tensor_weights() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) IteratedConvergenceMover (class in pyrosetta.rosetta.protocols.moves) iteration() (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) iterations() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) itime() (in module pyrosetta.rosetta.ObjexxFCL) itoa() (in module pyrosetta.rosetta.protocols.sparta) ivalue() (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) izstream (class in pyrosetta.rosetta.utility.io)