Index – W

w (pyrosetta.rosetta.basic.gpu.float4 property) (pyrosetta.rosetta.basic.sampling.orientations.Quaternion property) W (pyrosetta.rosetta.core.chemical.element.Elements attribute) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj property) w (pyrosetta.rosetta.protocols.simple_filters.Quat property) w() (in module pyrosetta.rosetta.numeric.statistics) (pyrosetta.rosetta.numeric.Quaternion_double_t method) W2I_1 (pyrosetta.rosetta.protocols.sparta.ANN property) W2I_2 (pyrosetta.rosetta.protocols.sparta.ANN property) W2I_3 (pyrosetta.rosetta.protocols.sparta.ANN property) W2L1_1 (pyrosetta.rosetta.protocols.sparta.ANN property) W2L1_2 (pyrosetta.rosetta.protocols.sparta.ANN property) W2L1_3 (pyrosetta.rosetta.protocols.sparta.ANN property) W2L2_1 (pyrosetta.rosetta.protocols.sparta.ANN property) W2L2_2 (pyrosetta.rosetta.protocols.sparta.ANN property) W2L2_3 (pyrosetta.rosetta.protocols.sparta.ANN property) w_ (pyrosetta.rosetta.numeric.urs_Quat property) w_dist() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) w_dist_ (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj property) w_im() (in module pyrosetta.rosetta.numeric.statistics) w_intra_ (pyrosetta.rosetta.core.scoring.elec.weight_triple property) w_squared() (pyrosetta.rosetta.numeric.Quaternion_double_t method) W_to_Ot (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) W_to_Ot_norm (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) W_to_Ot_norm2 (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) W_to_Ot_norm3 (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) wadj (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj property) wait_for_remote_vars() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) WAITING_ON_DEPENDENCIES (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) 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) walk_along_x() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) walk_along_y() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) walk_along_z() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) WalkingBondAnglePerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) WalkingPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) wallpaper_group() (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) WallpaperGroup (class in pyrosetta.rosetta.protocols.cryst) WallpaperGroupSetting (class in pyrosetta.rosetta.protocols.cryst) WARN (pyrosetta.rosetta.core.select.residue_selector.slice_enums.OutOfBoundsMode attribute) Warning (pyrosetta.rosetta.basic.MemTracer property) (pyrosetta.rosetta.basic.MemTracerImpl property) (pyrosetta.rosetta.basic.Tracer property) (pyrosetta.rosetta.basic.TracerImpl property) Warning() (in module pyrosetta.rosetta.basic) warning_messages() (pyrosetta.rosetta.utility.tag.XMLValidationOutput method) warnings() (pyrosetta.rosetta.utility.tag.XMLErrorHandler method) (pyrosetta.rosetta.utility.tag.XMLValidationOutput method) was_cyclic_model_created (pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo property) 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) was_visited() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) wat_desolv (pyrosetta.rosetta.core.scoring.ScoreType attribute) wat_entropy (pyrosetta.rosetta.core.scoring.ScoreType attribute) WATER (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) water_adduct_hbond_score() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) water_adjust() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) water_atom_interaction_cutoff() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) water_atom_interaction_cutoff2() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) water_clashes() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) water_dielectric() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) water_hybrid_sf() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) water_occlusions() (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) water_offset_for_atom() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype method) water_oxygen_clashes_with_residue() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) WATER_PACKING_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) water_pseudo_thickness() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) water_sol_values() (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) water_specific_hbond_energy() (in module pyrosetta.rosetta.protocols.hydrate) water_steepness() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) water_thickness() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) water_water_bridge_cutoff2() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) water_xyz (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.MyWaterHolder property) WaterAdductHBondEnergy (class in pyrosetta.rosetta.core.energy_methods) WaterAdductHBondEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) WaterAdductHBondPotential (class in pyrosetta.rosetta.core.scoring) WaterAdductIntraEnergy (class in pyrosetta.rosetta.core.energy_methods) WaterAdductIntraEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) WaterAnchorInfo (class in pyrosetta.rosetta.core.pack.rotamer_set) WaterBuilder (class in pyrosetta.rosetta.core.scoring.lkball) WaterBuilderForRestype (class in pyrosetta.rosetta.core.scoring.lkball) WaterFeatures (class in pyrosetta.rosetta.protocols.features) WaterFeaturesCreator (class in pyrosetta.rosetta.protocols.features) WaterMediatedHbondMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) WaterMediatedHbondMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) WaterPackingInfo (class in pyrosetta.rosetta.core.pack.rotamer_set) WaterRot (class in pyrosetta.rosetta.protocols.simple_moves) WaterRotsDB (class in pyrosetta.rosetta.protocols.simple_moves) waters() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBAtom method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) WaterSpecificEnergy (class in pyrosetta.rosetta.core.energy_methods) WaterSpecificEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) WaterWeightGridSet (class in pyrosetta.rosetta.core.energy_methods) WATSON_CRICK (pyrosetta.rosetta.core.chemical.rna.BaseEdge attribute) WatsonCrickResidueMatcher (class in pyrosetta.rosetta.core.conformation) WatsonCrickRotamerCouplings (class in pyrosetta.rosetta.protocols.dna) WatsonCrickRotamerCouplingsCreator (class in pyrosetta.rosetta.protocols.dna) wbb_bb_ (pyrosetta.rosetta.core.scoring.elec.weight_triple property) wbb_sc_ (pyrosetta.rosetta.core.scoring.elec.weight_triple property) wc_edge_paired() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) WC_STACKED_PAIR (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) weak_ptr_basic_datacache_CacheableData_t (class in pyrosetta.rosetta.std) weak_ptr_const_basic_datacache_HierarchicalDataMap_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_chemical_AtomTypeSet_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_chemical_ElementSet_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_chemical_MMAtomTypeSet_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_chemical_ResidueType_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_chemical_ResidueTypeSet_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_conformation_Conformation_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_environment_EnvCore_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_environment_FoldTreeSketch_Node_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_kinematics_AtomTree_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_scoring_etable_Etable_t (class in pyrosetta.rosetta.std) weak_ptr_const_core_scoring_etable_MembEtable_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_environment_Environment_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_enzdes_EnzdesFlexBBProtocol_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_enzdes_SecondaryMatchProtocol_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_flexpack_rotamer_set_FlexbbRotamerSets_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_forge_build_BuildInstruction_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_jd3_JGJobNode_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_topology_broker_TopologyBroker_t (class in pyrosetta.rosetta.std) weak_ptr_const_protocols_topology_broker_TopologyClaimer_t (class in pyrosetta.rosetta.std) weak_ptr_const_utility_tag_Tag_t (class in pyrosetta.rosetta.std) weak_ptr_core_chemical_ResidueType_t (class in pyrosetta.rosetta.std) weak_ptr_core_conformation_Conformation_t (class in pyrosetta.rosetta.std) weak_ptr_core_conformation_parametric_Parameter_t (class in pyrosetta.rosetta.std) weak_ptr_core_conformation_parametric_Parameters_t (class in pyrosetta.rosetta.std) weak_ptr_core_conformation_parametric_ParametersSet_t (class in pyrosetta.rosetta.std) weak_ptr_core_conformation_parametric_ParametrizationCalculator_t (class in pyrosetta.rosetta.std) weak_ptr_core_conformation_Residue_t (class in pyrosetta.rosetta.std) weak_ptr_core_environment_FoldTreeSketch_Node_t (class in pyrosetta.rosetta.std) weak_ptr_core_kinematics_tree_Atom_t (class in pyrosetta.rosetta.std) weak_ptr_core_pose_Pose_t (class in pyrosetta.rosetta.std) weak_ptr_core_pose_reference_pose_ReferencePose_t (class in pyrosetta.rosetta.std) weak_ptr_core_pose_reference_pose_ReferencePoseSet_t (class in pyrosetta.rosetta.std) weak_ptr_numeric_ClusteringTreeNode_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_abinitio_Templates_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_environment_Environment_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSets_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_forge_components_VarLengthBuild_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_frag_picker_FragmentPicker_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_frag_picker_VallChunk_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_frag_picker_VallProvider_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_helical_bundle_BackboneGridSamplerHelper_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_helical_bundle_BundleGridSamplerHelper_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_jd2_JobInputter_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_jd3_JGJobNode_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_jd3_JGResultNode_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_moves_Mover_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_noesy_assign_Resonance_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_optimize_weights_WrapperOptEMultifunc_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_topology_broker_TopologyBroker_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_topology_broker_TopologyClaimer_t (class in pyrosetta.rosetta.std) weak_ptr_protocols_vardist_solaccess_VarSolDistSasaCalculator_t (class in pyrosetta.rosetta.std) weak_ptr_utility_tag_Tag_t (class in pyrosetta.rosetta.std) weak_ptr_utility_tag_XMLSchemaRepeatableCTNode_t (class in pyrosetta.rosetta.std) weight (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions property) weight() (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGrid method) Weight() (pyrosetta.rosetta.basic.sampling.orientations.QuatSet method) weight() (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.pose.rna.RNA_Datum method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) (pyrosetta.rosetta.core.scoring.func.TopOutFunc method) (pyrosetta.rosetta.core.scoring.hbonds.HBond method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.SmallAtNb method) (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.ConstAbinitioMoverWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.LargeFragWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.SmallFragWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.SmoothFragWeight method) weight_ (pyrosetta.rosetta.protocols.jumping.JumpSelector.JumpWeightDef property) weight_func() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) weight_map() (pyrosetta.rosetta.protocols.pose_metric_calculators.EnergiesData method) WEIGHT_Tab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) weight_triple (class in pyrosetta.rosetta.core.scoring.elec) weight_type_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) weight_type_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) weighted_atom_pair_energy() (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) weighted_average() (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) weighted_center() (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) weighted_energy_map() (pyrosetta.rosetta.protocols.pose_metric_calculators.EnergiesData method) weighted_energy_map_vector() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) weighted_string_of() (pyrosetta.rosetta.core.scoring.EMapVector method) weighted_sum() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) weighted_total() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.EnergiesData method) weighted_total_no_master() (pyrosetta.rosetta.protocols.pose_metric_calculators.EnergiesData method) weighted_total_no_master_vector() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) weighted_total_vector() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) WeightedFragmentSmoothTrialMover (class in pyrosetta.rosetta.protocols.hybridization) WeightedFragmentTrialMover (class in pyrosetta.rosetta.protocols.hybridization) WeightedSampler (class in pyrosetta.rosetta.numeric.random) weightFileName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) WeightRangeConstraint (class in pyrosetta.rosetta.protocols.optimize_weights) weights() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.numeric.random.WeightedSampler method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) weights_ (pyrosetta.rosetta.protocols.sic_dock.CBScore property) weights_for_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) well_depth() (pyrosetta.rosetta.core.scoring.func.SquareWell2Func method) (pyrosetta.rosetta.core.scoring.func.SquareWellFunc method) wfa_atr() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) wfa_rep() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) wfa_sol() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) wgCUBIC (pyrosetta.rosetta.protocols.cryst.WallpaperGroupSetting attribute) wgHEXAGONAL (pyrosetta.rosetta.protocols.cryst.WallpaperGroupSetting attribute) wgMONOCLINIC (pyrosetta.rosetta.protocols.cryst.WallpaperGroupSetting attribute) wgNOSETTING (pyrosetta.rosetta.protocols.cryst.WallpaperGroupSetting attribute) wgTETRAGONAL (pyrosetta.rosetta.protocols.cryst.WallpaperGroupSetting attribute) what() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree 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.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.std.exception method) (pyrosetta.rosetta.std.ios_base.failure method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) whatIsTooSmall() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) where_is_line() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) which_ (pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList property) which_atom_in_hbond (class in pyrosetta.rosetta.core.scoring.hbonds) which_bin_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) which_bin_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) which_chain() (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) which_glycosidic_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) which_hb_aatm (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) which_hb_abase (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) which_hb_abase2 (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) which_hb_abase_prime (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) which_hb_datm (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) which_hb_hatm (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) which_hb_unassigned (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) which_last_donor_atm (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) which_point_for_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) which_sheet() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) which_side() (pyrosetta.rosetta.core.pose.rna.BaseStack method) (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) which_ssElement() (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) which_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) WhileMover (class in pyrosetta.rosetta.protocols.moves) White (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) who_am_i() (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.Base method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_1A method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_1B method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2A method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2A2B method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2B method) whoami() (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) whole_line (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) whole_sc (pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType attribute) whole_structure_types() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) whole_whole (pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType attribute) WholeBodyRotationMover (class in pyrosetta.rosetta.protocols.rigid) WholeBodyTranslationMover (class in pyrosetta.rosetta.protocols.rigid) WholeStructureEnergy (class in pyrosetta.rosetta.core.scoring.methods) WI_1 (pyrosetta.rosetta.protocols.sparta.ANN property) WI_2 (pyrosetta.rosetta.protocols.sparta.ANN property) WI_3 (pyrosetta.rosetta.protocols.sparta.ANN property) widget_name() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.multistate_design.PosTypeCreator method) WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t (class in pyrosetta.rosetta.utility.factory) width (pyrosetta.rosetta.core.chemical.rna.GaussianParameter property) width() (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.numeric.IOTraits_double_t static method) (pyrosetta.rosetta.numeric.IOTraits_float_t static method) (pyrosetta.rosetta.numeric.IOTraits_int_t static method) (pyrosetta.rosetta.numeric.IOTraits_long_double_t static method) (pyrosetta.rosetta.numeric.IOTraits_long_t static method) (pyrosetta.rosetta.numeric.IOTraits_short_t static method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_int_t static method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_long_t static method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_short_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_double_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_float_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_int_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_long_double_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_long_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_short_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_int_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_long_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_short_t static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.std.ios_base method) WidthFirstSlidingWindowLoopClosure (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) wignerSynthesis() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) wignerSynthesisDiffSign() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) wignerSynthesisSameSign() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) wild_type (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info property) window_width_ (pyrosetta.rosetta.protocols.pose_sewing.filters.CSSettings property) WindowPoseCompMotifMetric (class in pyrosetta.rosetta.protocols.pose_sewing.simple_metrics) WindowPoseCompMotifMetricCreator (class in pyrosetta.rosetta.protocols.pose_sewing.simple_metrics) winning_address_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) winning_tag_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) wipe_out_moving_residues() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) wistream (class in pyrosetta.rosetta.std) wistream.sentry (class in pyrosetta.rosetta.std) with_lock() (in module pyrosetta.distributed) with_traceback() (pyrosetta.network.rosetta_udp_to_tcp_bridge.StartUpError method) (pyrosetta.PyRosettaException method) within1bonds_sets_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) within2bonds_sets_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) WL1_1 (pyrosetta.rosetta.protocols.sparta.ANN property) WL1_2 (pyrosetta.rosetta.protocols.sparta.ANN property) WL1_3 (pyrosetta.rosetta.protocols.sparta.ANN property) WL2_1 (pyrosetta.rosetta.protocols.sparta.ANN property) WL2_2 (pyrosetta.rosetta.protocols.sparta.ANN property) WL2_3 (pyrosetta.rosetta.protocols.sparta.ANN property) WobbleMover (class in pyrosetta.rosetta.protocols.simple_moves) work_motif_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) work_partition() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) work_template_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) worker_extra() (in module pyrosetta.distributed.dask) WORKING (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) working_align_res (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) working_best_alignment() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_block_stack_above_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_block_stack_below_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_bridge_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_calc_rms_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_fixed_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_floating_base_anchor_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_force_anti_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_force_north_sugar_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_force_south_sugar_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_force_syn_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_global_sample_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_minimize_res() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) working_moving_partition_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_moving_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_moving_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_moving_suite() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_moving_suite_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_native_alignment() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_native_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer 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) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) working_protonated_H1_adenosine_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_reference_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method)

working_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_sequence() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_superimpose_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) working_terminal_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) workingSetGen() (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet method) WorkUnit_BatchRelax (class in pyrosetta.rosetta.protocols.relax) WorkUnit_BatchRelax.WU_Header (class in pyrosetta.rosetta.protocols.relax) WorkUnit_BatchRelax_and_PostRescore (class in pyrosetta.rosetta.protocols.relax) WorkUnit_BatchRelax_and_PostRescore.WU_Header (class in pyrosetta.rosetta.protocols.relax) WorkUnit_bbGauss (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_bbGauss.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_CombinePose (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_CombinePose.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_FragInsert (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_FragInsert.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_KicCloser (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_KicCloser.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_LoopHash (class in pyrosetta.rosetta.protocols.loophash) (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_LoopHash.WU_Header (class in pyrosetta.rosetta.protocols.loophash) (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_MD (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_MD.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_MoverWrapper (class in pyrosetta.rosetta.protocols.wum) WorkUnit_MoverWrapper.WU_Header (class in pyrosetta.rosetta.protocols.wum) WorkUnit_NormalMode (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_NormalMode.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_PartialAbinitio (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_PartialAbinitio.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_RamaPerturber (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_RamaPerturber.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_Relax (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_Relax.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_Sampler (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_Sampler.WU_Header (class in pyrosetta.rosetta.protocols.mpi_refinement) WorkUnit_SilentStructStore (class in pyrosetta.rosetta.protocols.wum) WorkUnit_SilentStructStore.WU_Header (class in pyrosetta.rosetta.protocols.wum) WorkUnit_Wait (class in pyrosetta.rosetta.protocols.wum) WorkUnit_Wait.WU_Header (class in pyrosetta.rosetta.protocols.wum) WorkUnitBase (class in pyrosetta.rosetta.protocols.wum) WorkUnitBase.WU_Header (class in pyrosetta.rosetta.protocols.wum) WorkUnitList (class in pyrosetta.rosetta.protocols.wum) WorkUnitManager (class in pyrosetta.rosetta.protocols.wum) WorkUnitQueue (class in pyrosetta.rosetta.protocols.wum) WorkUnitQueue_Swapped (class in pyrosetta.rosetta.protocols.wum) Worst9merFilter (class in pyrosetta.rosetta.protocols.simple_filters) Worst9merFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) worst_distance() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) wostream (class in pyrosetta.rosetta.std) wostream.sentry (class in pyrosetta.rosetta.std) Wradius (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) Wradius() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) wrapped() (pyrosetta.rosetta.utility.options.OptionCollection static method) WrappedBaseChemistry (class in pyrosetta.rosetta.protocols.chemistries) WrappedOptEExpressionCreator (class in pyrosetta.rosetta.protocols.optimize_weights) WrapperOptEMultifunc (class in pyrosetta.rosetta.protocols.optimize_weights) write() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t method) (pyrosetta.rosetta.basic.ComparingTracer method) (pyrosetta.rosetta.basic.database.schema_generator.Schema method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerToFile method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.io.serialization.BUFFER method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.environment.AutoCutData method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.std.ostream method) (pyrosetta.rosetta.std.ostringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wostream method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.tag.Tag method) write2pdb() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter 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_alignments_to_file() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) write_all() (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) write_all_citations_and_unpublished_author_info() (pyrosetta.rosetta.basic.citation_manager.CitationManager method) write_all_citations_and_unpublished_author_info_from_list_to_stream() (pyrosetta.rosetta.basic.citation_manager.CitationManager method) write_all_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) write_apolar_hydrogens() (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) write_assignment() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_assignment_indent() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_assignment_stats() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_assignments() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_atom_names() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_atom_type_set_to_database() (pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO method) write_atompot (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) write_backbone_hydrogens() (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) write_batch_reports_table() (in module pyrosetta.rosetta.protocols.features) write_beam() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) write_beam_lps() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) write_binary() (in module pyrosetta.rosetta.core.io.serialization) (pyrosetta.rosetta.core.scoring.motif.XformScore method) write_binary_chars() (in module pyrosetta.rosetta.core.io.serialization) write_calc_values() (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) 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_charge (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) write_checkpoint() (in module pyrosetta.rosetta.protocols.dna) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) (pyrosetta.rosetta.protocols.multistate_design.SingleStateEntityData method) write_circle_intersection_mask_to_kinemage() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) write_clique_to_db() (pyrosetta.rosetta.protocols.features.ModelFeatures method) write_comment() (pyrosetta.rosetta.core.io.silent.SilentFileData method) write_complex_type_to_schema() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) write_connollySurface_to_pdb() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) write_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) write_coords() (pyrosetta.rosetta.core.conformation.ConformationKinWriter method) write_crick_params_file_data() (in module pyrosetta.rosetta.protocols.helical_bundle) write_current_state_to_state_array() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) write_data() (pyrosetta.rosetta.core.fragment.FragmentIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) write_database() (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) write_database_to_file() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) write_db() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) write_ddG_table_schema() (pyrosetta.rosetta.protocols.features.DdGFeatures method) write_debug_pdb() (in module pyrosetta.rosetta.protocols.glycopeptide_docking) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder method) WRITE_DECOYS_TO_HIERARCHY (pyrosetta.rosetta.basic.ProfTag attribute) 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_diel (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) write_dot_kinemage() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) write_downstream_coordinates() (pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) write_dynamic_rsr() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) write_edges_for_segment() (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) write_eggshell_to_pdb() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) write_eggshell_to_pdb_file() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) write_entities_checkpoint() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) write_espGrid_to_pdb() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) write_exposed_dots_to_kinemage() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) write_failures() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) write_failures_set() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) write_features_reporters_table() (in module pyrosetta.rosetta.protocols.features) write_file() (pyrosetta.io.silent_file_map.SilentFileMap method) write_formatted() (in module pyrosetta.rosetta.utility.json_spirit) write_generations_checkpoint() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) write_glycan_pdb_codes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) write_graphviz() (in module pyrosetta.rosetta.core.chemical) write_grid_to_file() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) write_grid_to_kinemage() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) 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.legacy_sewing) write_header() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_headers_to_hierarchy() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) write_hist_to_file() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) write_hist_to_stream() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) write_hydrogens() (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) write_info_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) write_info_to_log() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) write_int_area() (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter 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_kappa (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) write_kin_header() (pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter method) (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) write_kinemage_header() (in module pyrosetta.rosetta.core.conformation) write_last_generated_to_disk() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential method) write_lines() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) write_loops_to_file() (pyrosetta.rosetta.protocols.loops.Loops method) write_loops_to_stream() (pyrosetta.rosetta.protocols.loops.Loops method) write_mainchain_scoretable_to_stream() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable 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_median_distance() (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter 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.legacy_sewing) write_motifs_binary() (in module pyrosetta.rosetta.core.scoring.motif) write_motifs_to_disk() (in module pyrosetta.rosetta.protocols.motifs) write_mse_summary() (pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder method) write_native_residue_file() (in module pyrosetta.rosetta.protocols.legacy_sewing) write_nil_assignment() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_number_of_electrostatic_interactions_of_residues_to_files() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_only_highest_VC() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_out_ (pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator property) write_output() (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputter method) (pyrosetta.rosetta.protocols.jd3.output.ResultOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) 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) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) write_pdb_parametric_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) write_pdb_title_section_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) write_pdbinfo_labels() (pyrosetta.rosetta.core.pose.PDBInfo method) write_peak() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_peak_files() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) write_phipsi() (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) write_pocketGrid_to_pdb() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) write_polar_hydrogens() (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) write_pose() (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) write_pot (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) write_potentials_for_individual_scoreterms() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) write_psipred_ss2() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) write_pssm() (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) write_pymol_string_to_pdb() (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) write_rama_of_AAs_to_a_file() (in module pyrosetta.rosetta.protocols.features.strand_assembly) write_rama_score_all() (pyrosetta.rosetta.core.scoring.Ramachandran method) (pyrosetta.rosetta.core.scoring.Ramachandran2B method) write_resfile() (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) write_residuetype_to_database() (pyrosetta.rosetta.core.chemical.ResidueDatabaseIO method) write_resonances() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_restype() (pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter method) write_ROSETTASCRIPTS_complex_type() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser static method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsSchemaValidator static method) write_rotamer_library() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) write_rsd_coords() (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) (pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter method) write_schema_to_database() (in module pyrosetta.rosetta.basic.database) write_schema_to_db() (pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO method) (pyrosetta.rosetta.core.chemical.ResidueDatabaseIO method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.BatchFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) (pyrosetta.rosetta.protocols.features.ProtocolFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) write_score_function_method_options_table_schema() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions static method) write_score_tracer() (in module pyrosetta.rosetta.protocols.jd2) write_scorefile() (pyrosetta.rosetta.protocols.dna.PDBOutput method) (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.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) write_seqres_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) write_silent_struct() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) write_smol (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) write_spanfile() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) write_store() (pyrosetta.protocols.h5_structure_store_provider.H5StructureStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider method) write_strength() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) write_struct() (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) write_structure_store() (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager method) write_stub() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) write_summary() (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) write_talos_format() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) write_tensor_info() (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) write_to_binary() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) write_to_binary_file() (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) write_to_BRIX() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) write_to_compact_array() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) write_to_database() (pyrosetta.rosetta.basic.database.insert_statement_generator.InsertGenerator method) write_to_disk() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) WRITE_TO_FILE (pyrosetta.rosetta.basic.ProfTag attribute) write_to_file() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary 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.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) write_to_pdb() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) write_to_stream() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist 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_to_string() (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) write_topology_file() (in module pyrosetta.rosetta.core.chemical) write_undefined_coef1() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) write_undefined_coef2() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) write_virtual_atoms() (pyrosetta.rosetta.core.conformation.ConformationKinWriter method) (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) (pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) write_xfres_binary() (in module pyrosetta.rosetta.core.scoring.motif) WRITEABLE_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) WriteableCacheableData (class in pyrosetta.rosetta.basic.datacache) WriteableCacheableDataCreator (class in pyrosetta.rosetta.basic.datacache) WriteableCacheableDataFactory (class in pyrosetta.rosetta.basic.datacache) WriteableCacheableMap (class in pyrosetta.rosetta.basic.datacache) WriteFileSFB (class in pyrosetta.rosetta.protocols.jd2) WriteFiltersToPose (class in pyrosetta.rosetta.protocols.simple_moves) WriteFiltersToPoseCreator (class in pyrosetta.rosetta.protocols.simple_moves) WriteKinemageOutputter (class in pyrosetta.rosetta.protocols.match.output) WriteLigandMolFile (class in pyrosetta.rosetta.protocols.ligand_docking) WriteLigandMolFileCreator (class in pyrosetta.rosetta.protocols.ligand_docking) writelpsstore() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) writeMRC() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) WriteOut_MpiFileBuffer (class in pyrosetta.rosetta.protocols.jd2) WriteSSEMover (class in pyrosetta.rosetta.protocols.simple_moves) WriteSSEMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) 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) WriteUpstreamCoordinateKinemage (class in pyrosetta.rosetta.protocols.match.output) WriteUpstreamHitKinemage (class in pyrosetta.rosetta.protocols.match.output) wRMSD() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) ws (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType attribute) wsc_bb_ (pyrosetta.rosetta.core.scoring.elec.weight_triple property) wsc_sc_ (pyrosetta.rosetta.core.scoring.elec.weight_triple property) wstreambuf (class in pyrosetta.rosetta.std) wt_aa() (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) WT_COMPLEXES_LIST_FILE (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData.DDG_Bind_File_Index attribute) wt_score_components() (pyrosetta.rosetta.protocols.ddg.ddGMover method) wt_unbound_score_components() (pyrosetta.rosetta.protocols.ddg.ddGMover method) WT_UNBOUNDS_LIST_FILE (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData.DDG_Bind_File_Index attribute) WTEBiasEnergy (class in pyrosetta.rosetta.protocols.canonical_sampling) WUM_MPI_DATA_BLOCK (pyrosetta.rosetta.protocols.wum.WUM_MPI_TAGS attribute) WUM_MPI_end (pyrosetta.rosetta.protocols.wum.WUM_MPI_TAGS attribute) WUM_MPI_REQUEST_WU (pyrosetta.rosetta.protocols.wum.WUM_MPI_TAGS attribute) WUM_MPI_SEND_WU (pyrosetta.rosetta.protocols.wum.WUM_MPI_TAGS attribute) WUM_MPI_SPINDOWN (pyrosetta.rosetta.protocols.wum.WUM_MPI_TAGS attribute) WUM_MPI_TAGS (class in pyrosetta.rosetta.protocols.wum) wwPDBJobOutputter (class in pyrosetta.rosetta.protocols.jd2)