Index – W

w() (in module pyrosetta.rosetta.numeric.statistics) W128_T (class in pyrosetta.rosetta) w_im() (in module pyrosetta.rosetta.numeric.statistics) wait_for_remote_vars() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) waiting_on_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) WalkingBondAnglePerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) WalkingPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) Warning() (in module pyrosetta.rosetta.basic) was_init_called() (in module pyrosetta.rosetta.basic) was_modified() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) was_successful() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) water_adduct_hbond_score() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) water_dielectric() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) water_specific_hbond_energy() (in module pyrosetta.rosetta.protocols.hydrate) WaterAdductHBondPotential (class in pyrosetta.rosetta.core.scoring) WaterBuilder (class in pyrosetta.rosetta.core.scoring.lkball) WaterFeaturesCreator (class in pyrosetta.rosetta.protocols.features) weight() (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) weight_func() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) weighted_string_of() (pyrosetta.rosetta.core.scoring.EMapVector method) weights() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) weights_for_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) wfa_atr() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) wfa_rep() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) wfa_sol() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) what() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) whatIsTooSmall() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) which_atom_in_hbond (class in pyrosetta.rosetta.core.scoring.hbonds) which_glycosidic_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) which_point_for_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) which_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) whoami() (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) whole_pose_context_enmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) whole_pose_context_enmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) whole_structure_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) WholeBodyRotationMover (class in pyrosetta.rosetta.protocols.rigid) WholeBodyTranslationMover (class in pyrosetta.rosetta.protocols.rigid) WholeStructureEnergy (class in pyrosetta.rosetta.core.scoring.methods) widget_name() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) width() (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) WidthFirstSlidingWindowLoopClosure (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) wipe_out_moving_residues() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) within1bonds_sets_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) within2bonds_sets_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) WobbleMover (class in pyrosetta.rosetta.protocols.simple_moves) working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) working_pack_res_was_inputted() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) working_parameters() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) working_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) WorkUnit_bbGauss (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_CombinePose (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_FragInsert (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_KicCloser (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_LoopHash (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_MD (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_MoverWrapper (class in pyrosetta.rosetta.protocols.wum) WorkUnit_NormalMode (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_PartialAbinitio (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_RamaPerturber (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_Relax (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_SilentStructStore (class in pyrosetta.rosetta.protocols.wum) WorkUnitBase (class in pyrosetta.rosetta.protocols.wum) WorkUnitList (class in pyrosetta.rosetta.protocols.wum) worst_distance() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) Wradius() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) wrapped() (pyrosetta.rosetta.utility.options.OptionCollection method) WrapperOptEMultifunc (class in pyrosetta.rosetta.protocols.optimize_weights) write() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) write2pdb() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) write_3Dprojection_kinemage() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) write_AA_distribution_with_direction_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_AA_distribution_without_direction_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_AA_kind_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_ab_H3_kink_metrics_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) write_ab_metrics_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) write_all() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) write_all_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) write_assignments() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) write_batch_reports_table() (in module pyrosetta.rosetta.protocols.features) write_binary() (in module pyrosetta.rosetta.core.io.serialization) write_binary_chars() (in module pyrosetta.rosetta.core.io.serialization) write_cdr_metrics_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) write_cdr_residue_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) write_chain_B_resNum_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_checkpoint() (in module pyrosetta.rosetta.protocols.dna) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) write_circle_intersection_mask_to_kinemage() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) write_comment() (pyrosetta.rosetta.core.io.silent.SilentFileData method) write_complex_type_to_schema() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) write_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) write_crick_params_file_data() (in module pyrosetta.rosetta.protocols.helical_bundle) write_db() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method)

write_definition() (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) write_downstream_coordinates() (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) write_eggshell_to_pdb() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) write_exposed_dots_to_kinemage() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) write_features_reporters_table() (in module pyrosetta.rosetta.protocols.features) write_formatted() (in module pyrosetta.rosetta.utility.json_spirit) write_glycan_pdb_codes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) write_graphviz() (in module pyrosetta.rosetta.core.chemical) write_Grid_to_pdb() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) write_grids() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) write_hashing_scores_to_file() (in module pyrosetta.rosetta.protocols.sewing) write_info_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) write_interface_residues_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) write_interface_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) write_interface_side_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) write_kinemage_header() (in module pyrosetta.rosetta.core.conformation) write_lines() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) write_loops_to_file() (pyrosetta.rosetta.protocols.loops.Loops method) write_loops_to_stream() (pyrosetta.rosetta.protocols.loops.Loops method) write_match_groups() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) write_match_scores() (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) write_metric_value() (in module pyrosetta.rosetta.basic) write_minor_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) write_model_file() (in module pyrosetta.rosetta.protocols.sewing) write_motifs_binary() (in module pyrosetta.rosetta.core.scoring.motif) write_number_of_electrostatic_interactions_of_residues_to_files() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_p_aa_pp_of_AAs_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_pdb_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) write_pdb_parametric_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) write_pocketGrid_to_pdb() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) write_psipred_ss2() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) write_pymol_string_to_pdb() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) write_rama_of_AAs_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_ROSETTASCRIPTS_complex_type() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) write_schema_to_database() (in module pyrosetta.rosetta.basic.database) write_schema_to_db() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) write_score_function_method_options_table_schema() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) write_score_tracer() (in module pyrosetta.rosetta.protocols.jd2) write_scorefile() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) write_silent_struct() (pyrosetta.rosetta.core.io.silent.SilentFileData method) write_talos_format() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) write_to_binary_file() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) write_to_disk() (pyrosetta.rosetta.protocols.sewing.Hasher method) write_to_file() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) write_to_pdb() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) write_to_stream() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) write_topology_file() (in module pyrosetta.rosetta.core.chemical) write_xfres_binary() (in module pyrosetta.rosetta.core.scoring.motif) WriteableCacheableData (class in pyrosetta.rosetta.basic.datacache) WriteableCacheableDataCreator (class in pyrosetta.rosetta.basic.datacache) WriteableCacheableMap (class in pyrosetta.rosetta.basic.datacache) WriteToDB_AA_to_terminal_loops() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_avg_b_factor_CB_at_each_component() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_dssp_ratio_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_ending_loop() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_hydrophobic_ratio_net_charge() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_long_strand_id_in_each_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_min_avg_dis_between_sheets_by_cen_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_min_dis_between_sheets_by_all_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_aro_AAs_in_a_pair_of_edge_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_charged_AAs_in_a_pair_of_edge_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_FWY_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_core_heading_W_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_edge_strands_in_each_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_of_sheets_that_surround_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_number_strands_in_each_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_prolines_that_seem_to_prevent_aggregation() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_ratio_of_core_heading_FWY_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_rkde() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_rkde_in_strands() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sandwich() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sandwich_by_AA_w_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sheet_antiparallel() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sheet_connectivity() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sheet_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_shortest_dis_between_facing_aro_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_starting_loop() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sw_can_by_sh() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_sw_res_size() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_topology_candidate() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_turn_AA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_turn_type() (in module pyrosetta.rosetta.protocols.features.strand_assembly) WriteToDB_whether_sw_is_not_connected_with_continuous_atoms() (in module pyrosetta.rosetta.protocols.features.strand_assembly) ws_methods_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ws_methods_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) wt_aa() (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) wwPDBJobOutputter (class in pyrosetta.rosetta.protocols.jd2)