Index – P

p1_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) p1_theta_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) p2_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) p_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) P_omega0() (in module pyrosetta.rosetta.numeric.crick_equations) pack_all_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) pack_and_minimize_linker_and_sidechains() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) pack_missing_sidechains() (in module pyrosetta.rosetta.core.pack) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) pack_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) pack_polar_hydrogens() (in module pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens) pack_residue() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) pack_rotamers() (in module pyrosetta.rosetta.core.pack) pack_rotamers_loop() (in module pyrosetta.rosetta.core.pack) pack_rotamers_run() (in module pyrosetta.rosetta.core.pack) pack_rotamers_setup() (in module pyrosetta.rosetta.core.pack) pack_scorefxn_pose_handshake() (in module pyrosetta.rosetta.core.pack) pack_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) packed_residues() (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) PackerEnergyAdd() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerEnergyMultiply() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerEnergySubtract() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerNeighborGraphFilter (class in pyrosetta.rosetta.protocols.simple_filters) PackerTask (class in pyrosetta.rosetta.core.pack.task) packertask() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) PackerTask_ (class in pyrosetta.rosetta.core.pack.task) packing_angle_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) packing_angle_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) PackingAngleEnum (class in pyrosetta.rosetta.protocols.antibody) PackRotamersMover (class in pyrosetta.rosetta.protocols.simple_moves) PackRotamersMoverLazy (class in pyrosetta.rosetta.protocols.simple_moves) PackRotamersMoverPartGreedy (class in pyrosetta.rosetta.protocols.enzdes) pad() (in module pyrosetta.rosetta.ObjexxFCL) pad_left() (in module pyrosetta.rosetta.utility) pad_results() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) pad_right() (in module pyrosetta.rosetta.utility) padded() (in module pyrosetta.rosetta.ObjexxFCL) pair_energy_H_v() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) pair_has_linkage_statistics() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) pair_sets_with_positions() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) paired() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) PairedSheetResidueSelector (class in pyrosetta.rosetta.protocols.denovo_design.residue_selectors) PairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) pairing_group_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) pairing_subelement_ct_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) PalesEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) parallel_base_test() (in module pyrosetta.rosetta.protocols.motifs) ParallelTempering (class in pyrosetta.rosetta.protocols.canonical_sampling) ParallelTemperingCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) param_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) param_index() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) Parameters (class in pyrosetta.rosetta.core.conformation.parametric) parameters() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) parameters_for_restype() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) parameters_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) ParametersSet (class in pyrosetta.rosetta.core.conformation.parametric) paratope_charge() (in module pyrosetta.rosetta.protocols.antibody) paratope_sasa() (in module pyrosetta.rosetta.protocols.antibody) ParatopeEpitopeSiteConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) ParatopeSiteConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) parent() (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.utility.file.PathName method) parent_node() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) parin_favorite_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) parse() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) parse_adduct_string() (in module pyrosetta.rosetta.core.chemical) parse_atom_pair_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) parse_atom_type_data() (in module pyrosetta.rosetta.core.chemical.sdf) parse_attributes_from_tag() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) parse_command_line() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) parse_constraint_generators() (in module pyrosetta.rosetta.protocols.constraint_generator) parse_coordinate_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) parse_database_connection() (in module pyrosetta.rosetta.basic.database) parse_default_and_user_options() (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) parse_dof_task_type() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) parse_dof_tasks() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) parse_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) parse_excluded_properites() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_excluded_types() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_filter() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) parse_gridset_tag() (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) parse_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) parse_included_properites() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_included_types() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) parse_length_string() (in module pyrosetta.rosetta.protocols.denovo_design) parse_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) parse_loops_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) parse_motif() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) parse_motif_string() (in module pyrosetta.rosetta.protocols.denovo_design) parse_movemap_factory() (in module pyrosetta.rosetta.core.select.movemap) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) parse_movemap_factory_legacy() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_my_tag() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptions method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector 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.cyclic_peptide.RamaMutationSelector 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.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.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptions method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) parse_named_movemap_factory_legacy() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_NMR_name() (in module pyrosetta.rosetta.core.scoring.constraints) parse_optional_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) parse_options() (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) parse_or_properties() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_orientations() (in module pyrosetta.rosetta.protocols.denovo_design.components) parse_out_non_standard_residues() (in module pyrosetta.rosetta.core.sequence) parse_PDBnum_icode() (in module pyrosetta.rosetta.core.pose) parse_plain_text_with_columns() (in module pyrosetta.rosetta.protocols.antibody.grafting) parse_protocol_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) parse_quota_command_line() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) parse_report_format_string() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) parse_resfile() (in module pyrosetta.rosetta.core.pack.task) parse_resfile_string() (in module pyrosetta.rosetta.core.pack.task) parse_resfile_string_with_no_lockdown() (in module pyrosetta.rosetta.protocols.forge.methods) parse_residue() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) parse_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_resnames() (in module pyrosetta.rosetta.protocols.helical_bundle) parse_resnum() (in module pyrosetta.rosetta.core.pose) parse_rotamer_sampling_data() (in module pyrosetta.rosetta.core.pack.task.operation) parse_score_function() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_seeds() (in module pyrosetta.rosetta.protocols.seeded_abinitio) parse_segment_names() (in module pyrosetta.rosetta.protocols.denovo_design.connection) parse_sequence() (in module pyrosetta.rosetta.core.pose) parse_string_to_boolean_expression() (in module pyrosetta.rosetta.numeric.expression_parser) parse_string_to_expression() (in module pyrosetta.rosetta.numeric.expression_parser) parse_stub_sets() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) parse_tag() (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) parse_task_operations() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_xyz_vector() (in module pyrosetta.rosetta.protocols.rosetta_scripts) partial_align() (in module pyrosetta.rosetta.protocols.hybridization) PartialSecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) Particle (class in pyrosetta.rosetta.core.optimization) ParticleSwarmMinimizer (class in pyrosetta.rosetta.core.optimization) partition_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) partition_by_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) partition_by_symm_jumps() (in module pyrosetta.rosetta.core.pose.symmetry) partition_coloring() (pyrosetta.rosetta.core.kinematics.FoldTree method) partition_definition() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) partition_pose_by_jump() (in module pyrosetta.rosetta.core.pose) Partner (class in pyrosetta.rosetta.protocols.rigid) partner() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) partner1() (pyrosetta.rosetta.protocols.contact_map.Contact method) partner2() (pyrosetta.rosetta.protocols.contact_map.Contact method) partners() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) pass_metropolis() (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) passes_com_vector_criterion() (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) passes_filter() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) passes_filters() (in module pyrosetta.rosetta.protocols.ligand_docking) passes_hardsphere_filter() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) Patch (class in pyrosetta.rosetta.core.chemical) patch_map() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) patch_name_from_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) patch_operation_from_patch_file_line() (in module pyrosetta.rosetta.core.chemical) PatchCase (class in pyrosetta.rosetta.core.chemical) PatchdockTransform (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) patched_name() (pyrosetta.rosetta.core.chemical.Patch method) patches() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) PatchOperation (class in pyrosetta.rosetta.core.chemical) path() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) path_basename() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) path_dist() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) path_distance() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) path_distances() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) PathName (class in pyrosetta.rosetta.utility.file) pathname() (in module pyrosetta.rosetta.utility) PathOption (class in pyrosetta.rosetta.utility.options) PathOptionKey (class in pyrosetta.rosetta.utility.options) PathVectorOption (class in pyrosetta.rosetta.utility.options) PathVectorOptionKey (class in pyrosetta.rosetta.utility.options) pb_bound_tag() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) pb_unbound_tag() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) pbest() (pyrosetta.rosetta.core.optimization.Particle method) PBP_clustering_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) PCluster (class in pyrosetta.rosetta.protocols.pockets) PClusterSet (class in pyrosetta.rosetta.protocols.pockets) PCS_data_input (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_data_input_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_data_input_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_data_input_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_data_input_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_experimental() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) PCS_file_data (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_file_data_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_file_data_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_file_data_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_file_data_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_FragDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) PCS_line_data (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_line_data_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_line_data_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_line_data_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_line_data_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_tolerance() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) PcsInputCenter (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsInputFile (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsInputLine (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) pd_reader() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) PDatom (class in pyrosetta.rosetta.core.scoring) pdb2pose() (pyrosetta.rosetta.core.pose.PDBInfo method) pdb_code_from_rosetta_name() (pyrosetta.rosetta.core.io.NomenclatureManager method) pdb_comments() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileRep method) pdb_end() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) pdb_info() (pyrosetta.rosetta.core.pose.Pose method) pdb_parents() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) pdb_start() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) pdb_to_pose() (in module pyrosetta.rosetta.core.pose) PdbDataFeaturesCreator (class in pyrosetta.rosetta.protocols.features) pdbid() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) PDBInfo (class in pyrosetta.rosetta.core.pose) PDBJobInputter (class in pyrosetta.rosetta.protocols.jd2) PDBJobOutputter (class in pyrosetta.rosetta.protocols.jd2) PDBLandmark (class in pyrosetta.rosetta.protocols.antibody) PDBNumbering (class in pyrosetta.rosetta.protocols.antibody.design) pdbpos() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) PDBPoseMap (class in pyrosetta.rosetta.core.pose) PDBSilentStructCreator (class in pyrosetta.rosetta.core.import_pose) pdbslice() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.magnesium) PDBTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) PDBTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) PDinter (class in pyrosetta.rosetta.core.scoring.power_diagram) PDsphere (class in pyrosetta.rosetta.core.scoring.power_diagram) PDvertex (class in pyrosetta.rosetta.core.scoring.power_diagram) peak_volume() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) PeakAssignment (class in pyrosetta.rosetta.protocols.noesy_assign) PeakAssignmentResidueMap (class in pyrosetta.rosetta.protocols.noesy_assign) peek() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) penalty() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) peptide_entry() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) peptide_length() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) PeptideDeriverBasicStreamOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverEntryType (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverFilter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverMarkdownStreamOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverOutputterContainer (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverPoseOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverReportFormat (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideStapleDesignMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) per_chain_renumbering() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) per_res_sc_sasa() (in module pyrosetta.rosetta.core.scoring.sasa) percent_native() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) perform_all_reactions() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) perform_major_reaction_only() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) performing_pure_insertion() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) performs_major_reaction_only() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) periodic_range() (in module pyrosetta.rosetta.basic) PeriodicBoundFunc (class in pyrosetta.rosetta.core.scoring.constraints) PeriodicFunc (class in pyrosetta.rosetta.core.scoring.func) periodicity() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) PerResidueInterfaceData (class in pyrosetta.rosetta.protocols.analysis) pert() (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) pert_size() (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) PertMinMover (class in pyrosetta.rosetta.protocols.simple_moves) PertType (class in pyrosetta.rosetta.protocols.helical_bundle) perturb() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_angles() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_backbone_for_test() (in module pyrosetta.rosetta.protocols.grafting) perturb_beta_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) perturb_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_c_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_ca_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_chain() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) perturb_lengths() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_n_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_omega() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_phi() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_psi() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_sequence() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_subset() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_subset_with_balance() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_torsions() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_weights() (pyrosetta.rosetta.core.scoring.ScoreFunction method) perturb_with_balance() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturbation_magnitude() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) perturbation_type() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) PerturbBundleOptions (class in pyrosetta.rosetta.protocols.helical_bundle) PerturbByBins (class in pyrosetta.rosetta.protocols.simple_moves.bin_transitions) PerturbChiSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) perturbed_sequence() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) Perturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) perturber() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) perturber_effect (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber) perturber_exhausted() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) perturber_type() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) PerturberSet (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) PerturbRotamerSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) pH_mode_exceptions() (in module pyrosetta.rosetta.core.chemical) phe_tyr_corrections() (in module pyrosetta.rosetta.protocols.make_rot_lib) Phi (class in pyrosetta.rosetta.protocols.frag_picker.scores) phi() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) phi_max() (pyrosetta.rosetta.core.sequence.ABEGO method) phi_min() (pyrosetta.rosetta.core.sequence.ABEGO method) PhiPsiRmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) PhiPsiSquareWell (class in pyrosetta.rosetta.protocols.frag_picker.scores) PhiSelector (class in pyrosetta.rosetta.core.select.residue_selector) phosphate_base_phosphate_rmsd() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) phosphate_base_phosphate_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) phosphate_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) PhosphateMover (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) pick() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) pick_and_apply() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) pick_and_cache_fragments() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) pick_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) pick_chunk_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) pick_fragments() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_fragments_by_ss() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_fragments_by_ss_plus_aa() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_loops_chainbreak() (in module pyrosetta.rosetta.protocols.comparative_modeling) pick_loops_unaligned() (in module pyrosetta.rosetta.protocols.comparative_modeling) pick_loopy_cutpoint() (in module pyrosetta.rosetta.core.kinematics) pick_new_cutpoints() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) pick_sequence_from_database() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) pick_solution() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) Picker (class in pyrosetta.rosetta.protocols.denovo_design.components) picking_rounds() (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) PIKAA (class in pyrosetta.rosetta.core.pack.task) PIKNA (class in pyrosetta.rosetta.core.pack.task) PIKRNA (class in pyrosetta.rosetta.core.pack.task) pivot1() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) pivot2() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) pivot_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) pivot_loop() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) pivot_residues() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) PivotPicker (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) place() (pyrosetta.rosetta.core.conformation.Residue method) place_atom_positions() (in module pyrosetta.rosetta.protocols.helical_bundle) place_de_novo_wat_at_anchor() (in module pyrosetta.rosetta.protocols.hydrate) place_stubs() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) placeholder_clone() (pyrosetta.rosetta.core.chemical.ResidueType method) placeholder_info() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) placeholder_residue() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) PlacementMinimizationMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceSimultaneouslyMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceStubMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlainPdbJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) PlainRawJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) PlainSilentFileJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) plus_plus() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) pmatch() (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) PocketConstraint (class in pyrosetta.rosetta.protocols.pockets) PocketConstraintCreator (class in pyrosetta.rosetta.protocols.pockets) PocketExemplarMultifunc (class in pyrosetta.rosetta.protocols.pockets) PocketGrid (class in pyrosetta.rosetta.protocols.pockets) point_for_nonchitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) point_on_ellipsoid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) points_for_nonchitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) POLAR (class in pyrosetta.rosetta.core.pack.task) polar_atom (class in pyrosetta.rosetta.protocols.hbnet) PolarHydrogenFilter (class in pyrosetta.rosetta.core.chemical) Policy (class in pyrosetta.rosetta.protocols.nonlocal) polycubic_interpolation() (in module pyrosetta.rosetta.core.pack.dunbrack) polymer_direction() (pyrosetta.rosetta.core.kinematics.Edge method) PolymerBondedEnergyContainer (class in pyrosetta.rosetta.core.scoring) PolymerBondedNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) PolymerBondedNeighborIterator (class in pyrosetta.rosetta.core.scoring) polymeric_oriented_sequence_distance() (pyrosetta.rosetta.core.conformation.Residue method) polymeric_sequence_distance() (pyrosetta.rosetta.core.conformation.Residue method) PoolEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) pop() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) pop_back() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) pop_passport() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) populate_all_cdrs() (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) populate_results_from_db() (in module pyrosetta.rosetta.protocols.antibody.grafting) pos() (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) pos_in_history_queue() (pyrosetta.rosetta.utility.recent_history_queue method) pos_mod() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.protocols.cryst) Pose (class in pyrosetta.rosetta.core.pose) pose() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval 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.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) pose1_has_most_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) pose2pdb() (pyrosetta.rosetta.core.pose.PDBInfo method) pose_aligner() (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) pose_cache_float_data() (pyrosetta.rosetta.core.io.StructFileRep method) pose_cache_string_data() (pyrosetta.rosetta.core.io.StructFileRep method) pose_charge() (in module pyrosetta.rosetta.protocols.antibody) pose_cop() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) pose_data_cache_from_sfr() (in module pyrosetta.rosetta.core.io) pose_energies_from_sfr() (in module pyrosetta.rosetta.core.io) pose_energies_to_json() (in module pyrosetta.rosetta.protocols.rpc) pose_energy() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) pose_from_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) pose_from_file() (in module pyrosetta.rosetta.core.import_pose) pose_from_job() (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) pose_from_pdb_stream() (in module pyrosetta.rosetta.core.import_pose) pose_from_pdbstring() (in module pyrosetta.rosetta.core.import_pose) pose_from_pose() (in module pyrosetta.rosetta.core.io) pose_from_rcsb() (in module pyrosetta.toolbox.rcsb) pose_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) pose_from_sequence() (in module pyrosetta.io) (in module pyrosetta.toolbox.mutants) pose_has_nonzero_Bs() (in module pyrosetta.rosetta.core.scoring.electron_density) pose_index() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) pose_input_stream() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) pose_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) pose_loop_anchors() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) pose_matches_user_tag() (in module pyrosetta.rosetta.protocols.jobdist) pose_max_nbr_radius() (in module pyrosetta.rosetta.core.pose) pose_num() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) pose_numbered() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) pose_raw_unfolded_state_energymap() (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) pose_residue_is_terminal() (in module pyrosetta.rosetta.core.pose) pose_right() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) pose_seq() (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) pose_setup_from_file() (in module pyrosetta.rosetta.protocols.recces) pose_setup_turner() (in module pyrosetta.rosetta.protocols.recces) pose_tilt_angle_and_center_distance() (in module pyrosetta.rosetta.protocols.membrane) pose_tm_com() (in module pyrosetta.rosetta.protocols.membrane) pose_to_pack_data() (in module pyrosetta.rosetta.core.scoring.packstat) pose_to_pdb() (in module pyrosetta.rosetta.core.pose) pose_to_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) pose_with_most_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) PoseArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) poseBfacts2multivec() (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) PoseComment (class in pyrosetta.rosetta.protocols.simple_filters) PoseCommentsFeaturesCreator (class in pyrosetta.rosetta.protocols.features) PoseConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) PoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) PoseFoundResiduesCombination (class in pyrosetta.rosetta.protocols.enzdes) PoseFromSFRBuilder (class in pyrosetta.rosetta.core.io.pose_from_sfr) PoseInfoFilter (class in pyrosetta.rosetta.protocols.simple_filters) PoseInputStreamJobInputter (class in pyrosetta.rosetta.protocols.jd2) PoseMatchOutputWriter (class in pyrosetta.rosetta.protocols.match.output) PoseMetricContainer (class in pyrosetta.rosetta.core.pose.metrics) PoseNumberedLoopFileReader (class in pyrosetta.rosetta.protocols.loops) poseOPs_from_files() (in module pyrosetta.rosetta.core.import_pose) PosePropertyReporterCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) PoseResidueTypeSet (class in pyrosetta.rosetta.core.chemical) poses_from_cmd_line() (in module pyrosetta.rosetta.protocols.comparative_modeling) poses_from_files() (in module pyrosetta.rosetta.core.import_pose) poses_from_silent() (in module pyrosetta.io) PoseSelectorCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) poseSphericalSamples() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) PoseToStructFileRepConverter (class in pyrosetta.rosetta.core.io.pose_to_sfr) position() (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) position_ala_ddG() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) position_cutpoint_phosphate_torsions() (in module pyrosetta.rosetta.core.pose.rna) position_data_begin() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) position_data_end() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) position_five_prime_phosphate() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) position_index() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) position_of_atom_on_ring() (in module pyrosetta.rosetta.core.conformation) position_untouchable() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) PositionConservedResiduesStore (class in pyrosetta.rosetta.core.pose.datacache) PositionDdGInfo (class in pyrosetta.rosetta.core.io.PositionDdGInfo) positions() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) positions_in_secstruct() (in module pyrosetta.rosetta.protocols.simple_filters) positions_incompatible_with_task() (in module pyrosetta.rosetta.protocols.backrub) PositionSpecificRandomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) PositionType (class in pyrosetta.rosetta.protocols.dna) positive() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) positive_pow() (in module pyrosetta.rosetta.core.pack.dunbrack) positive_value() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) possible_root() (in module pyrosetta.rosetta.protocols.rna.denovo) (pyrosetta.rosetta.core.kinematics.FoldTree method) PossibleAtomTypesForAtom (class in pyrosetta.rosetta.core.chemical.gasteiger) possibly_canonical() (in module pyrosetta.rosetta.core.chemical.rna) possibly_canonical_strict() (in module pyrosetta.rosetta.core.chemical.rna) post_catalog_op() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) post_relax_round_update_steps() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) pow() (in module pyrosetta.rosetta.ObjexxFCL) power() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) power_distance() (in module pyrosetta.rosetta.core.scoring.power_diagram) PowerDiagram (class in pyrosetta.rosetta.core.scoring.power_diagram) PP() (in module pyrosetta.rosetta.numeric.crick_equations) ppo_torsion_bin (class in pyrosetta.rosetta.core.conformation) PQR (class in pyrosetta.rosetta.core.scoring) pre_catalog_op() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) pre_chitip_transform() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) pre_load_data() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) pre_process() (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) pre_relax_round_update_steps() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) preallocate() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) preamble() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) preapply() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) precision() (pyrosetta.rosetta.core.io.silent.SilentStruct method) precompute_transforms() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) predefine_search() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) Predicate (class in pyrosetta.rosetta.core.scoring) PredictedBurialFnEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) preexisting_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) preferred_root_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) prefix() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.utility.options.OptionCollection method) preload_motif_data() (in module pyrosetta.rosetta.core.scoring.motif) prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) prepare_for_match_enumeration() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) prepare_for_output() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) prepare_for_output_writing() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) prepare_for_packing() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) prepare_for_simulated_annealing() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) prepare_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) prepare_rotamers_for_packing() (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) prepare_scoring() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) prepare_scratch_residue() (in module pyrosetta.rosetta.core.pose.rna) prepare_silent_struct() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) prepare_to_note_hits_for_completed_round() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) PrepareForCentroid (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) PrepareForFullatom (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) prepend_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) prepend_new_residues() (in module pyrosetta.rosetta.protocols.denovo_design.components) prepend_output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) prepend_polymer_residue_before_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) prepend_res() (pyrosetta.rosetta.core.pose.PDBInfo method) PrependMainchainAtom (class in pyrosetta.rosetta.core.chemical) preprocess_data() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) preserve_atom_coords() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) preserve_c_beta() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) preserve_crystinfo() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) preserve_detailed_balance() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) preserve_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) pretty() (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) pretty_print_atomicoor() (in module pyrosetta.rosetta.core.chemical) pretty_print_rd() (in module pyrosetta.rosetta.protocols.make_rot_lib) prevent_repacking() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) PreventChainFromRepackingOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) PreventRepacking (class in pyrosetta.rosetta.core.pack.task.operation) PreventResiduesFromRepackingOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) previous() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) previous_child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) previous_round_geometry_still_matchable() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) previous_sibling() (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) previous_working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) PrimarySequenceNeighborhoodSelector (class in pyrosetta.rosetta.core.select.residue_selector) principal_angle_degrees() (in module pyrosetta.rosetta.numeric) principal_components_and_eigenvalues_ndimensions() (in module pyrosetta.rosetta.numeric) PrincipalQuantumNumber_strings() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) print() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.frag_picker.nonlocal.NonlocalPair method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE 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.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid 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.sewing.ModelNode method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) print_all_bond_lengths() (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) print_all_types() (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) print_allowed_types() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) print_atom_pair_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) print_backbone_torsions() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) print_base_centroid_atoms_for_rb_entropy() (in module pyrosetta.rosetta.protocols.recces) print_base_state() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_bondangles() (pyrosetta.rosetta.core.chemical.ResidueType method) print_chis() (in module pyrosetta.rosetta.core.chemical) print_comments() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_conformation() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_current_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) print_debug() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) print_dihedrals() (pyrosetta.rosetta.core.chemical.ResidueType method) print_dofs() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) print_fragment() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_fragment_index() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_fragment_seq() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_generators() (in module pyrosetta.rosetta.core.scoring.power_diagram) print_hbonds() (in module pyrosetta.rosetta.protocols.rna.denovo) print_header() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_headers() (in module pyrosetta.rosetta.protocols.hbnet) print_information() (in module pyrosetta.rosetta.protocols.rosetta_scripts) print_internal_coords() (in module pyrosetta.rosetta.protocols.rna.denovo) print_list_to_string() (in module pyrosetta.rosetta.protocols.hbnet) print_metric() (pyrosetta.rosetta.core.pose.Pose method) print_network() (in module pyrosetta.rosetta.protocols.hbnet) print_network_w_pdb_numbering() (in module pyrosetta.rosetta.protocols.hbnet) print_parent_remarks() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_partners() (in module pyrosetta.rosetta.core.scoring.power_diagram) print_point() (in module pyrosetta.rosetta.numeric.kdtree) print_points() (in module pyrosetta.rosetta.numeric.kdtree) print_pretty_path_distances() (pyrosetta.rosetta.core.chemical.ResidueType method) print_probabilities() (in module pyrosetta.rosetta.numeric) print_report() (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) print_residue_numbers() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_residues_near_water() (in module pyrosetta.rosetta.protocols.hydrate) print_score() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) print_score_header() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_scores() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_submotif_info() (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_sugar_pucker_state() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_template_script() (in module pyrosetta.rosetta.protocols.rosetta_scripts) print_torsion_info() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_tree() (in module pyrosetta.rosetta.numeric.kdtree) print_vertex_groups() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) print_vertices() (in module pyrosetta.rosetta.core.scoring.power_diagram) (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.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) print_WorkingParameters_info() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) priority() (pyrosetta.rosetta.basic.Tracer method) private_data_to_public_array() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) private_index() (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) prob() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) prob_random_pert_current() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) prob_sum_of_gaussians() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) prob_uniform() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) prob_withinrot() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) probability() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) probability_limit() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) probe_radius_for_atom_type() (in module pyrosetta.rosetta.protocols.match) ProbeRadius (class in pyrosetta.rosetta.protocols.match) process() (in module pyrosetta.rosetta.basic.options) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) process_decoy() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) process_deletions() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) process_hit() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) process_input_file() (in module pyrosetta.rosetta.protocols.rna.denovo) process_insertions() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) process_matches() (pyrosetta.rosetta.protocols.match.Matcher method) product() (in module pyrosetta.rosetta.core.pack.dunbrack) (in module pyrosetta.rosetta.numeric) prof_reset() (in module pyrosetta.rosetta.basic) prof_show() (in module pyrosetta.rosetta.basic) prof_start_function_body() (in module pyrosetta.rosetta.basic) prof_stop_function_body() (in module pyrosetta.rosetta.basic) profile() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) profile_struct() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ProfileScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreBlosum62 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreDistWeight (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreL1 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreStructL1 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreSubMatrix (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProgressBarObserver (class in pyrosetta.rosetta.protocols.canonical_sampling) ProgressBarObserverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) prohibit_single_residue_loops() (pyrosetta.rosetta.protocols.loops.LoopsFileOptions method) projection_matrix() (in module pyrosetta.rosetta.numeric) projperp() (in module pyrosetta.rosetta.protocols.sic_dock) ProlinePhiScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) promote_sameresidue_child_of_jump_atom() (in module pyrosetta.rosetta.core.conformation)

promote_sameresidue_nonjump_child() (pyrosetta.rosetta.core.kinematics.AtomTree method) properties() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) properties_match_this() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) property() (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) property_from_string() (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) property_penalty() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) property_set_indices_matching_residue() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) proposal_density() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) proposed_since_last_batch() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) protein_atom_name_to_num() (in module pyrosetta.rosetta.core.scoring.rna) protein_dielectric() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) protein_interface_design() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) ProteinBackboneAtomAtomPairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinBackboneTorsionAngleFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinBondGeometryFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinInterfaceDesignOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) ProteinInterfaceMultiStateDesignMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) ProteinLigandInterfaceUpweighter (class in pyrosetta.rosetta.protocols.enzdes) ProteinResidueConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinRMSDFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinRMSDNoSuperpositionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinSilentStruct_SinglePrecCreator (class in pyrosetta.rosetta.core.io.silent) ProteinSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) protocol_option_set() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) proton_chi_2_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) proton_chi_extra_samples() (pyrosetta.rosetta.core.chemical.ResidueType method) proton_chi_samples() (pyrosetta.rosetta.core.chemical.ResidueType method) proton_tolerance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) ProtonResonance (class in pyrosetta.rosetta.protocols.noesy_assign) provide_attributes() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) provide_stored_derivatives() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) provide_xml_schema() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover 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.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator 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.AtomPairConstraintGenerator 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.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.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.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.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector 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.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator 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.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.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.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover 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.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover 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.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator 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.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins 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.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator 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.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) ProxySentinel (class in pyrosetta.rosetta.ObjexxFCL.internal) prune_cavity_balls() (in module pyrosetta.rosetta.core.scoring.packstat) prune_hidden_cavity_balls() (in module pyrosetta.rosetta.core.scoring.packstat) psc_compare() (in module pyrosetta.rosetta.core.pack.dunbrack) pseudobonds() (pyrosetta.rosetta.core.conformation.Residue method) Psi (class in pyrosetta.rosetta.protocols.frag_picker.scores) psi() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) psi_max() (pyrosetta.rosetta.core.sequence.ABEGO method) psi_min() (pyrosetta.rosetta.core.sequence.ABEGO method) public_array_to_private_data() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) push() (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) push_back() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) push_back_and_finalize() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) push_front() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) push_passport() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) push_to_front_of_history_queue() (pyrosetta.rosetta.utility.recent_history_queue method) put() (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) put_in_cutpoint() (in module pyrosetta.rosetta.core.import_pose) put_intra_into_total() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) put_jump_stubs_intra_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) putback() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) PValuedFragmentScoreManager (class in pyrosetta.rosetta.protocols.frag_picker.scores) PyEnergyMethodRegistrator (class in pyrosetta.rosetta.core.scoring.methods) PyExitCallback (class in pyrosetta.rosetta.utility.py) PyReturnValuePolicyTest_DummyClassCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_DummyClassOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_PoseCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_PoseOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionCOP2() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_SF_ReplicaCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_SF_ReplicaOP() (in module pyrosetta.rosetta.protocols.toolbox) pyrosetta (module) pyrosetta.io (module) pyrosetta.logging_support (module) pyrosetta.method_bindings (module) pyrosetta.method_bindings.pose (module) pyrosetta.rosetta (module) pyrosetta.rosetta.basic (module) pyrosetta.rosetta.basic.database (module) pyrosetta.rosetta.basic.database.insert_statement_generator (module) pyrosetta.rosetta.basic.database.schema_generator (module) pyrosetta.rosetta.basic.datacache (module) pyrosetta.rosetta.basic.gpu (module) pyrosetta.rosetta.basic.mpi (module) pyrosetta.rosetta.basic.options (module) pyrosetta.rosetta.basic.resource_manager (module) pyrosetta.rosetta.basic.resource_manager.fallback_configuration (module) pyrosetta.rosetta.basic.resource_manager.locator (module) pyrosetta.rosetta.basic.sampling (module) pyrosetta.rosetta.basic.sampling.orientations (module) pyrosetta.rosetta.basic.svd (module) pyrosetta.rosetta.core (module) pyrosetta.rosetta.core.chemical (module) pyrosetta.rosetta.core.chemical.carbohydrates (module) pyrosetta.rosetta.core.chemical.element (module) pyrosetta.rosetta.core.chemical.gasteiger (module) pyrosetta.rosetta.core.chemical.mainchain_potential (module) pyrosetta.rosetta.core.chemical.mmCIF (module) pyrosetta.rosetta.core.chemical.NucleotideTools (module) pyrosetta.rosetta.core.chemical.orbitals (module) pyrosetta.rosetta.core.chemical.rings (module) pyrosetta.rosetta.core.chemical.rna (module) pyrosetta.rosetta.core.chemical.rotamers (module) pyrosetta.rosetta.core.chemical.sdf (module) pyrosetta.rosetta.core.conformation (module) pyrosetta.rosetta.core.conformation.carbohydrates (module) pyrosetta.rosetta.core.conformation.membrane (module) pyrosetta.rosetta.core.conformation.orbitals (module) pyrosetta.rosetta.core.conformation.parametric (module) pyrosetta.rosetta.core.conformation.residue_datacache (module) pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType (module) pyrosetta.rosetta.core.conformation.signals (module) pyrosetta.rosetta.core.conformation.symmetry (module) pyrosetta.rosetta.core.environment (module) pyrosetta.rosetta.core.enzymes (module) pyrosetta.rosetta.core.fragment (module) pyrosetta.rosetta.core.fragment.picking_old (module) pyrosetta.rosetta.core.fragment.picking_old.concepts (module) pyrosetta.rosetta.core.fragment.picking_old.vall (module) pyrosetta.rosetta.core.fragment.picking_old.vall.eval (module) pyrosetta.rosetta.core.fragment.picking_old.vall.gen (module) pyrosetta.rosetta.core.fragment.picking_old.vall.scores (module) pyrosetta.rosetta.core.grid (module) pyrosetta.rosetta.core.id (module) pyrosetta.rosetta.core.import_pose (module) pyrosetta.rosetta.core.import_pose.atom_tree_diffs (module) pyrosetta.rosetta.core.import_pose.pose_stream (module) pyrosetta.rosetta.core.indexed_structure_store (module) pyrosetta.rosetta.core.init (module) pyrosetta.rosetta.core.io (module) pyrosetta.rosetta.core.io.carbohydrates (module) pyrosetta.rosetta.core.io.external (module) pyrosetta.rosetta.core.io.mmcif (module) pyrosetta.rosetta.core.io.pdb (module) pyrosetta.rosetta.core.io.pose_from_sfr (module) pyrosetta.rosetta.core.io.pose_to_sfr (module) pyrosetta.rosetta.core.io.PositionDdGInfo (module) pyrosetta.rosetta.core.io.raw_data (module) pyrosetta.rosetta.core.io.rna (module) pyrosetta.rosetta.core.io.sequence_comparation (module) pyrosetta.rosetta.core.io.serialization (module) pyrosetta.rosetta.core.io.silent (module) pyrosetta.rosetta.core.kinematics (module) pyrosetta.rosetta.core.kinematics.tree (module) pyrosetta.rosetta.core.membrane (module) pyrosetta.rosetta.core.optimization (module) pyrosetta.rosetta.core.optimization.symmetry (module) pyrosetta.rosetta.core.pack (module) pyrosetta.rosetta.core.pack.annealer (module) pyrosetta.rosetta.core.pack.dunbrack (module) pyrosetta.rosetta.core.pack.dunbrack.cenrot (module) pyrosetta.rosetta.core.pack.interaction_graph (module) pyrosetta.rosetta.core.pack.rotamer_set (module) pyrosetta.rosetta.core.pack.rotamer_set.symmetry (module) pyrosetta.rosetta.core.pack.rotamers (module) pyrosetta.rosetta.core.pack.scmin (module) pyrosetta.rosetta.core.pack.task (module) pyrosetta.rosetta.core.pack.task.operation (module) pyrosetta.rosetta.core.pack.task.residue_selector (module) pyrosetta.rosetta.core.pack.task.rna (module) pyrosetta.rosetta.core.pose (module) pyrosetta.rosetta.core.pose.carbohydrates (module) pyrosetta.rosetta.core.pose.copydofs (module) pyrosetta.rosetta.core.pose.datacache (module) pyrosetta.rosetta.core.pose.full_model_info (module) pyrosetta.rosetta.core.pose.metrics (module) pyrosetta.rosetta.core.pose.metrics.simple_calculators (module) pyrosetta.rosetta.core.pose.motif (module) pyrosetta.rosetta.core.pose.ncbb (module) pyrosetta.rosetta.core.pose.reference_pose (module) pyrosetta.rosetta.core.pose.rna (module) pyrosetta.rosetta.core.pose.signals (module) pyrosetta.rosetta.core.pose.symmetry (module) pyrosetta.rosetta.core.scoring (module) pyrosetta.rosetta.core.scoring.aa_composition_energy (module) pyrosetta.rosetta.core.scoring.aa_repeat_energy (module) pyrosetta.rosetta.core.scoring.annealing (module) pyrosetta.rosetta.core.scoring.bin_transitions (module) pyrosetta.rosetta.core.scoring.carbohydrates (module) pyrosetta.rosetta.core.scoring.carbon_hbonds (module) pyrosetta.rosetta.core.scoring.constraints (module) pyrosetta.rosetta.core.scoring.cryst (module) pyrosetta.rosetta.core.scoring.custom_pair_distance (module) pyrosetta.rosetta.core.scoring.disulfides (module) pyrosetta.rosetta.core.scoring.dna (module) pyrosetta.rosetta.core.scoring.dssp (module) pyrosetta.rosetta.core.scoring.elec (module) pyrosetta.rosetta.core.scoring.elec.electrie (module) pyrosetta.rosetta.core.scoring.electron_density (module) pyrosetta.rosetta.core.scoring.electron_density_atomwise (module) pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType (module) pyrosetta.rosetta.core.scoring.etable (module) pyrosetta.rosetta.core.scoring.etable.coulomb (module) pyrosetta.rosetta.core.scoring.etable.count_pair (module) pyrosetta.rosetta.core.scoring.etable.etrie (module) pyrosetta.rosetta.core.scoring.fiber_diffraction (module) pyrosetta.rosetta.core.scoring.func (module) pyrosetta.rosetta.core.scoring.geometric_solvation (module) pyrosetta.rosetta.core.scoring.hackaro (module) pyrosetta.rosetta.core.scoring.hbonds (module) pyrosetta.rosetta.core.scoring.hbonds.hbtrie (module) pyrosetta.rosetta.core.scoring.interface_ (module) pyrosetta.rosetta.core.scoring.lkball (module) pyrosetta.rosetta.core.scoring.lkball.lkbtrie (module) pyrosetta.rosetta.core.scoring.loop_graph (module) pyrosetta.rosetta.core.scoring.loop_graph.evaluator (module) pyrosetta.rosetta.core.scoring.magnesium (module) pyrosetta.rosetta.core.scoring.membrane (module) pyrosetta.rosetta.core.scoring.methods (module) pyrosetta.rosetta.core.scoring.methods.carbohydrates (module) pyrosetta.rosetta.core.scoring.methods.dfire (module) pyrosetta.rosetta.core.scoring.mm (module) pyrosetta.rosetta.core.scoring.mm.mmtrie (module) pyrosetta.rosetta.core.scoring.motif (module) pyrosetta.rosetta.core.scoring.nv (module) pyrosetta.rosetta.core.scoring.orbitals (module) pyrosetta.rosetta.core.scoring.packing (module) pyrosetta.rosetta.core.scoring.packstat (module) pyrosetta.rosetta.core.scoring.packstat.old (module) pyrosetta.rosetta.core.scoring.power_diagram (module) pyrosetta.rosetta.core.scoring.rna (module) pyrosetta.rosetta.core.scoring.rna.chemical_shift (module) pyrosetta.rosetta.core.scoring.rna.data (module) pyrosetta.rosetta.core.scoring.sasa (module) pyrosetta.rosetta.core.scoring.saxs (module) pyrosetta.rosetta.core.scoring.sc (module) pyrosetta.rosetta.core.scoring.solid_surface (module) pyrosetta.rosetta.core.scoring.sym_e (module) pyrosetta.rosetta.core.scoring.symmetry (module) pyrosetta.rosetta.core.scoring.trie (module) pyrosetta.rosetta.core.scoring.vdwaals (module) pyrosetta.rosetta.core.select (module) pyrosetta.rosetta.core.select.jump_selector (module) pyrosetta.rosetta.core.select.movemap (module) pyrosetta.rosetta.core.select.residue_selector (module) pyrosetta.rosetta.core.select.util (module) pyrosetta.rosetta.core.sequence (module) pyrosetta.rosetta.core.util (module) pyrosetta.rosetta.cppdb (module) pyrosetta.rosetta.numeric (module) pyrosetta.rosetta.numeric.conversions (module) pyrosetta.rosetta.numeric.crick_equations (module) pyrosetta.rosetta.numeric.expression_parser (module) pyrosetta.rosetta.numeric.fourier (module) pyrosetta.rosetta.numeric.geometry (module) pyrosetta.rosetta.numeric.geometry.hashing (module) pyrosetta.rosetta.numeric.histograms (module) pyrosetta.rosetta.numeric.interpolation (module) pyrosetta.rosetta.numeric.interpolation.spline (module) pyrosetta.rosetta.numeric.kdtree (module) pyrosetta.rosetta.numeric.kinematic_closure (module) pyrosetta.rosetta.numeric.kinematic_closure.radians (module) pyrosetta.rosetta.numeric.linear_algebra (module) pyrosetta.rosetta.numeric.model_quality (module) pyrosetta.rosetta.numeric.nls (module) pyrosetta.rosetta.numeric.random (module) pyrosetta.rosetta.numeric.statistics (module) pyrosetta.rosetta.ObjexxFCL (module) pyrosetta.rosetta.ObjexxFCL.bit (module) pyrosetta.rosetta.ObjexxFCL.format (module) pyrosetta.rosetta.ObjexxFCL.Fortran (module) pyrosetta.rosetta.ObjexxFCL.internal (module) pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator (module) pyrosetta.rosetta.protocols (module) pyrosetta.rosetta.protocols.aa_composition (module) pyrosetta.rosetta.protocols.abinitio (module) pyrosetta.rosetta.protocols.abinitio.abscript (module) pyrosetta.rosetta.protocols.analysis (module) pyrosetta.rosetta.protocols.anchored_design (module) pyrosetta.rosetta.protocols.antibody (module) pyrosetta.rosetta.protocols.antibody.clusters (module) pyrosetta.rosetta.protocols.antibody.constraints (module) pyrosetta.rosetta.protocols.antibody.design (module) pyrosetta.rosetta.protocols.antibody.grafting (module) pyrosetta.rosetta.protocols.antibody.residue_selector (module) pyrosetta.rosetta.protocols.antibody.snugdock (module) pyrosetta.rosetta.protocols.antibody.task_operations (module) pyrosetta.rosetta.protocols.antibody_legacy (module) pyrosetta.rosetta.protocols.backbone_moves (module) pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover (module) pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers (module) pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers (module) pyrosetta.rosetta.protocols.backrub (module) pyrosetta.rosetta.protocols.branch_angle (module) pyrosetta.rosetta.protocols.canonical_sampling (module) pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks (module) pyrosetta.rosetta.protocols.carbohydrates (module) pyrosetta.rosetta.protocols.cartesian (module) pyrosetta.rosetta.protocols.checkpoint (module) pyrosetta.rosetta.protocols.cluster (module) pyrosetta.rosetta.protocols.cluster.calibur (module) pyrosetta.rosetta.protocols.comparative_modeling (module) pyrosetta.rosetta.protocols.comparative_modeling.features (module) pyrosetta.rosetta.protocols.constraint_generator (module) pyrosetta.rosetta.protocols.constraints_additional (module) pyrosetta.rosetta.protocols.contact_map (module) pyrosetta.rosetta.protocols.coupled_moves (module) pyrosetta.rosetta.protocols.cryst (module) pyrosetta.rosetta.protocols.cyclic_peptide (module) pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker (module) pyrosetta.rosetta.protocols.cyclic_peptide_predict (module) pyrosetta.rosetta.protocols.ddG (module) pyrosetta.rosetta.protocols.ddg (module) pyrosetta.rosetta.protocols.denovo_design (module) pyrosetta.rosetta.protocols.denovo_design.architects (module) pyrosetta.rosetta.protocols.denovo_design.components (module) pyrosetta.rosetta.protocols.denovo_design.connection (module) pyrosetta.rosetta.protocols.denovo_design.constraints (module) pyrosetta.rosetta.protocols.denovo_design.filters (module) pyrosetta.rosetta.protocols.denovo_design.movers (module) pyrosetta.rosetta.protocols.denovo_design.residue_selectors (module) pyrosetta.rosetta.protocols.denovo_design.task_operations (module) pyrosetta.rosetta.protocols.design_opt (module) pyrosetta.rosetta.protocols.dna (module) pyrosetta.rosetta.protocols.docking (module) pyrosetta.rosetta.protocols.docking.membrane (module) pyrosetta.rosetta.protocols.docking.stateless (module) pyrosetta.rosetta.protocols.domain_assembly (module) pyrosetta.rosetta.protocols.electron_density (module) pyrosetta.rosetta.protocols.environment (module) pyrosetta.rosetta.protocols.environment.claims (module) pyrosetta.rosetta.protocols.enzdes (module) pyrosetta.rosetta.protocols.enzdes.enzutil (module) pyrosetta.rosetta.protocols.enzymatic_movers (module) pyrosetta.rosetta.protocols.evaluation (module) pyrosetta.rosetta.protocols.evolution (module) pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools (module) pyrosetta.rosetta.protocols.features (module) pyrosetta.rosetta.protocols.features.helixAssembly (module) pyrosetta.rosetta.protocols.features.RelevantResiduesMode (module) pyrosetta.rosetta.protocols.features.strand_assembly (module) pyrosetta.rosetta.protocols.fibril (module) pyrosetta.rosetta.protocols.filters (module) pyrosetta.rosetta.protocols.fldsgn (module) pyrosetta.rosetta.protocols.fldsgn.filters (module) pyrosetta.rosetta.protocols.fldsgn.potentials (module) pyrosetta.rosetta.protocols.fldsgn.potentials.sspot (module) pyrosetta.rosetta.protocols.fldsgn.topology (module) pyrosetta.rosetta.protocols.flexpack (module) pyrosetta.rosetta.protocols.flexpack.annealer (module) pyrosetta.rosetta.protocols.flexpack.interaction_graph (module) pyrosetta.rosetta.protocols.flexpack.rotamer_set (module) pyrosetta.rosetta.protocols.flexpep_docking (module) pyrosetta.rosetta.protocols.floppy_tail (module) pyrosetta.rosetta.protocols.flxbb (module) pyrosetta.rosetta.protocols.fold_from_loops (module) pyrosetta.rosetta.protocols.forge (module) pyrosetta.rosetta.protocols.forge.build (module) pyrosetta.rosetta.protocols.forge.build.BuildInstructionState (module) pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme (module) pyrosetta.rosetta.protocols.forge.components (module) pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage (module) pyrosetta.rosetta.protocols.forge.constraints (module) pyrosetta.rosetta.protocols.forge.methods (module) pyrosetta.rosetta.protocols.forge.remodel (module) pyrosetta.rosetta.protocols.frag_picker (module) pyrosetta.rosetta.protocols.frag_picker.nonlocal (module) pyrosetta.rosetta.protocols.frag_picker.quota (module) pyrosetta.rosetta.protocols.frag_picker.scores (module) pyrosetta.rosetta.protocols.frags (module) pyrosetta.rosetta.protocols.generalized_kinematic_closure (module) pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter (module) pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber (module) pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector (module) pyrosetta.rosetta.protocols.genetic_algorithm (module) pyrosetta.rosetta.protocols.geometry (module) pyrosetta.rosetta.protocols.grafting (module) pyrosetta.rosetta.protocols.grafting.simple_movers (module) pyrosetta.rosetta.protocols.hbnet (module) pyrosetta.rosetta.protocols.helical_bundle (module) pyrosetta.rosetta.protocols.helical_bundle.parameters (module) pyrosetta.rosetta.protocols.helix_capper (module) pyrosetta.rosetta.protocols.hotspot_hashing (module) pyrosetta.rosetta.protocols.hotspot_hashing.movers (module) pyrosetta.rosetta.protocols.hybridization (module) pyrosetta.rosetta.protocols.hydrate (module) pyrosetta.rosetta.protocols.idealize (module) pyrosetta.rosetta.protocols.indel (module) pyrosetta.rosetta.protocols.indexed_structure_store (module) pyrosetta.rosetta.protocols.indexed_structure_store.filters (module) pyrosetta.rosetta.protocols.init (module) pyrosetta.rosetta.protocols.interface (module) pyrosetta.rosetta.protocols.jd2 (module) pyrosetta.rosetta.protocols.jd2.archive (module) pyrosetta.rosetta.protocols.jd2.JobInputterInputSource (module) pyrosetta.rosetta.protocols.jobdist (module) pyrosetta.rosetta.protocols.jumping (module) pyrosetta.rosetta.protocols.kinematic_closure (module) pyrosetta.rosetta.protocols.kinematic_closure.perturbers (module) pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers (module) pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers (module) pyrosetta.rosetta.protocols.kinmatch (module) pyrosetta.rosetta.protocols.ligand_docking (module) pyrosetta.rosetta.protocols.ligand_docking.ligand_options (module) pyrosetta.rosetta.protocols.ligand_docking.rdf (module) pyrosetta.rosetta.protocols.loop_build (module) pyrosetta.rosetta.protocols.loop_grower (module) pyrosetta.rosetta.protocols.loop_modeler (module) pyrosetta.rosetta.protocols.loop_modeler.perturbers (module) pyrosetta.rosetta.protocols.loop_modeling (module) pyrosetta.rosetta.protocols.loop_modeling.refiners (module) pyrosetta.rosetta.protocols.loop_modeling.samplers (module) pyrosetta.rosetta.protocols.loop_modeling.utilities (module) pyrosetta.rosetta.protocols.loophash (module) pyrosetta.rosetta.protocols.loops (module) pyrosetta.rosetta.protocols.loops.filters (module) pyrosetta.rosetta.protocols.loops.loop_closure (module) pyrosetta.rosetta.protocols.loops.loop_closure.ccd (module) pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure (module) pyrosetta.rosetta.protocols.loops.loop_mover (module) pyrosetta.rosetta.protocols.loops.loop_mover.perturb (module) pyrosetta.rosetta.protocols.loops.loop_mover.refine (module) pyrosetta.rosetta.protocols.loops.loops_definers (module) pyrosetta.rosetta.protocols.magnesium (module) pyrosetta.rosetta.protocols.make_rot_lib (module) pyrosetta.rosetta.protocols.match (module) pyrosetta.rosetta.protocols.match.downstream (module) pyrosetta.rosetta.protocols.match.output (module) pyrosetta.rosetta.protocols.match.upstream (module) pyrosetta.rosetta.protocols.matdes (module) pyrosetta.rosetta.protocols.md (module) pyrosetta.rosetta.protocols.mean_field (module) pyrosetta.rosetta.protocols.medal (module) pyrosetta.rosetta.protocols.membrane (module) pyrosetta.rosetta.protocols.membrane.benchmark (module) pyrosetta.rosetta.protocols.membrane.geometry (module) pyrosetta.rosetta.protocols.membrane.symmetry (module) pyrosetta.rosetta.protocols.membrane.visualize (module) pyrosetta.rosetta.protocols.metal_interface (module) pyrosetta.rosetta.protocols.motif_grafting (module) pyrosetta.rosetta.protocols.motif_grafting.movers (module) pyrosetta.rosetta.protocols.motifs (module) pyrosetta.rosetta.protocols.moves (module) pyrosetta.rosetta.protocols.mpi_refinement (module) pyrosetta.rosetta.protocols.multistate_design (module) pyrosetta.rosetta.protocols.ncbb (module) pyrosetta.rosetta.protocols.ncbb.oop (module) pyrosetta.rosetta.protocols.neighbor (module) pyrosetta.rosetta.protocols.noesy_assign (module) pyrosetta.rosetta.protocols.nonlocal (module) pyrosetta.rosetta.protocols.normalmode (module) pyrosetta.rosetta.protocols.optimize_weights (module) pyrosetta.rosetta.protocols.pack_daemon (module) pyrosetta.rosetta.protocols.parser (module) pyrosetta.rosetta.protocols.pb_potential (module) pyrosetta.rosetta.protocols.peptide_deriver (module) pyrosetta.rosetta.protocols.pmut_scan (module) pyrosetta.rosetta.protocols.pockets (module) pyrosetta.rosetta.protocols.pose_length_moves (module) pyrosetta.rosetta.protocols.pose_reporters (module) pyrosetta.rosetta.protocols.pose_selectors (module) pyrosetta.rosetta.protocols.protein_interface_design (module) pyrosetta.rosetta.protocols.protein_interface_design.filters (module) pyrosetta.rosetta.protocols.protein_interface_design.movers (module) pyrosetta.rosetta.protocols.qsar (module) pyrosetta.rosetta.protocols.qsar.scoring_grid (module) pyrosetta.rosetta.protocols.rbsegment_relax (module) pyrosetta.rosetta.protocols.recces (module) pyrosetta.rosetta.protocols.recces.options (module) pyrosetta.rosetta.protocols.recces.params (module) pyrosetta.rosetta.protocols.recces.sampler (module) pyrosetta.rosetta.protocols.recces.sampler.rna (module) pyrosetta.rosetta.protocols.recces.scratch (module) pyrosetta.rosetta.protocols.relax (module) pyrosetta.rosetta.protocols.relax.membrane (module) pyrosetta.rosetta.protocols.residue_optimization (module) pyrosetta.rosetta.protocols.residue_selectors (module) pyrosetta.rosetta.protocols.rigid (module) pyrosetta.rosetta.protocols.rna (module) pyrosetta.rosetta.protocols.rna.denovo (module) pyrosetta.rosetta.protocols.rna.denovo.base_pairs (module) pyrosetta.rosetta.protocols.rna.denovo.coarse (module) pyrosetta.rosetta.protocols.rna.denovo.fragments (module) pyrosetta.rosetta.protocols.rna.denovo.libraries (module) pyrosetta.rosetta.protocols.rna.denovo.movers (module) pyrosetta.rosetta.protocols.rna.denovo.options (module) pyrosetta.rosetta.protocols.rna.denovo.output (module) pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy (module) pyrosetta.rosetta.protocols.rna.denovo.setup (module) pyrosetta.rosetta.protocols.rna.movers (module) pyrosetta.rosetta.protocols.rna.setup (module) pyrosetta.rosetta.protocols.rosetta_scripts (module) pyrosetta.rosetta.protocols.rotamer_recovery (module) pyrosetta.rosetta.protocols.RotamerDump (module) pyrosetta.rosetta.protocols.rpc (module) pyrosetta.rosetta.protocols.sasa_scores (module) pyrosetta.rosetta.protocols.scoring (module) pyrosetta.rosetta.protocols.scoring.methods (module) pyrosetta.rosetta.protocols.scoring.methods.pcs (module) pyrosetta.rosetta.protocols.scoring.methods.pcs2 (module) pyrosetta.rosetta.protocols.scoring.methods.pcsTs1 (module) pyrosetta.rosetta.protocols.scoring.methods.pcsTs2 (module) pyrosetta.rosetta.protocols.scoring.methods.pcsTs3 (module) pyrosetta.rosetta.protocols.scoring.methods.pcsTs4 (module) pyrosetta.rosetta.protocols.scoring.methods.saxs (module) pyrosetta.rosetta.protocols.seeded_abinitio (module) pyrosetta.rosetta.protocols.sewing (module) pyrosetta.rosetta.protocols.sewing.sampling (module) pyrosetta.rosetta.protocols.sewing.sampling.requirements (module) pyrosetta.rosetta.protocols.sewing.scoring (module) pyrosetta.rosetta.protocols.sic_dock (module) pyrosetta.rosetta.protocols.sic_dock.scores (module) pyrosetta.rosetta.protocols.simple_filters (module) pyrosetta.rosetta.protocols.simple_moves (module) pyrosetta.rosetta.protocols.simple_moves.a3b_hbs (module) pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock (module) pyrosetta.rosetta.protocols.simple_moves.bb_sampler (module) pyrosetta.rosetta.protocols.simple_moves.bin_transitions (module) pyrosetta.rosetta.protocols.simple_moves.chiral (module) pyrosetta.rosetta.protocols.simple_moves.hbs (module) pyrosetta.rosetta.protocols.simple_moves.oop (module) pyrosetta.rosetta.protocols.simple_moves.rational_mc (module) pyrosetta.rosetta.protocols.simple_moves.sidechain_moves (module) pyrosetta.rosetta.protocols.simple_moves.symmetry (module) pyrosetta.rosetta.protocols.simple_moves.triazolamer (module) pyrosetta.rosetta.protocols.sparta (module) pyrosetta.rosetta.protocols.ss_prediction (module) pyrosetta.rosetta.protocols.star (module) pyrosetta.rosetta.protocols.stepwise (module) pyrosetta.rosetta.protocols.stepwise.legacy (module) pyrosetta.rosetta.protocols.stepwise.legacy.modeler (module) pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein (module) pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna (module) pyrosetta.rosetta.protocols.stepwise.legacy.screener (module) pyrosetta.rosetta.protocols.stepwise.modeler (module) pyrosetta.rosetta.protocols.stepwise.modeler.align (module) pyrosetta.rosetta.protocols.stepwise.modeler.movemap (module) pyrosetta.rosetta.protocols.stepwise.modeler.options (module) pyrosetta.rosetta.protocols.stepwise.modeler.packer (module) pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens (module) pyrosetta.rosetta.protocols.stepwise.modeler.precomputed (module) pyrosetta.rosetta.protocols.stepwise.modeler.protein (module) pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker (module) pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body (module) pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar (module) pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.options (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna (module) pyrosetta.rosetta.protocols.stepwise.monte_carlo.submotif (module) pyrosetta.rosetta.protocols.stepwise.options (module) pyrosetta.rosetta.protocols.stepwise.sampler (module) pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs (module) pyrosetta.rosetta.protocols.stepwise.sampler.input_streams (module) pyrosetta.rosetta.protocols.stepwise.sampler.jump (module) pyrosetta.rosetta.protocols.stepwise.sampler.protein (module) pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body (module) pyrosetta.rosetta.protocols.stepwise.sampler.rna (module) pyrosetta.rosetta.protocols.stepwise.sampler.screener (module) pyrosetta.rosetta.protocols.stepwise.screener (module) pyrosetta.rosetta.protocols.stepwise.setup (module) pyrosetta.rosetta.protocols.struct_fragment (module) pyrosetta.rosetta.protocols.surface_docking (module) pyrosetta.rosetta.protocols.symmetric_docking (module) pyrosetta.rosetta.protocols.symmetric_docking.membrane (module) pyrosetta.rosetta.protocols.toolbox (module) pyrosetta.rosetta.protocols.toolbox.match_enzdes_util (module) pyrosetta.rosetta.protocols.toolbox.pose_manipulation (module) pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators (module) pyrosetta.rosetta.protocols.toolbox.rigid_body (module) pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations (module) pyrosetta.rosetta.protocols.toolbox.sample_around (module) pyrosetta.rosetta.protocols.toolbox.task_operations (module) pyrosetta.rosetta.protocols.topology_broker (module) pyrosetta.rosetta.protocols.topology_broker.claims (module) pyrosetta.rosetta.protocols.topology_broker.weights (module) pyrosetta.rosetta.protocols.trajectory (module) pyrosetta.rosetta.protocols.ub_e2c (module) pyrosetta.rosetta.protocols.unfolded_state_energy_calculator (module) pyrosetta.rosetta.protocols.viewer (module) pyrosetta.rosetta.protocols.viewer.graphics_states_param (module) pyrosetta.rosetta.protocols.vip (module) pyrosetta.rosetta.protocols.wum (module) pyrosetta.rosetta.std (module) pyrosetta.rosetta.utility (module) pyrosetta.rosetta.utility.excn (module) pyrosetta.rosetta.utility.factory (module) pyrosetta.rosetta.utility.file (module) pyrosetta.rosetta.utility.graph (module) pyrosetta.rosetta.utility.has_insertion_operator_implementation (module) pyrosetta.rosetta.utility.io (module) pyrosetta.rosetta.utility.io.mpi_stream (module) pyrosetta.rosetta.utility.json_spirit (module) pyrosetta.rosetta.utility.keys (module) pyrosetta.rosetta.utility.libsvm (module) pyrosetta.rosetta.utility.options (module) pyrosetta.rosetta.utility.py (module) pyrosetta.rosetta.utility.signals (module) pyrosetta.rosetta.utility.sql_database (module) pyrosetta.rosetta.utility.tag (module) pyrosetta.rosetta.utility.tools (module) pyrosetta.rosetta.utility.xsd_util (module) pyrosetta.teaching (module) pyrosetta.toolbox (module) pyrosetta.toolbox.cleaning (module) pyrosetta.toolbox.extract_coords_pose (module) pyrosetta.toolbox.generate_resfile (module) pyrosetta.toolbox.mutants (module) pyrosetta.toolbox.numpy_utils (module) pyrosetta.toolbox.rcsb (module) pyrosetta.util (module) PyTracer (class in pyrosetta.rosetta.basic)