Index – D

d() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) d1() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) d2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) d2s() (pyrosetta.rosetta.utility.subset_mapping method) d_array_scale() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) d_hbond_weight_dE() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) data() (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) data_dim() (in module pyrosetta.rosetta.protocols.recces) data_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) data_ptr() (pyrosetta.rosetta.core.conformation.Residue method) database_dir() (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) database_directory() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) database_fname() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) database_mode_from_name() (in module pyrosetta.rosetta.utility.sql_database) DatabaseJobInputter (class in pyrosetta.rosetta.protocols.features) DatabaseJobOutputter (class in pyrosetta.rosetta.protocols.features) DatabaseResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) DatabaseResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) DatabaseThread (class in pyrosetta.rosetta.protocols.toolbox.task_operations) DataLoader (class in pyrosetta.rosetta.protocols.parser) DataLoaderCreator (class in pyrosetta.rosetta.protocols.parser) DataLoaderFactory (class in pyrosetta.rosetta.protocols.parser) DataMap (class in pyrosetta.rosetta.basic.datacache) DataPoint (class in pyrosetta.rosetta.protocols.cluster) datatype() (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) date() (in module pyrosetta.rosetta.ObjexxFCL) Dawson() (in module pyrosetta.rosetta.numeric.statistics) dB_dBdnmtr() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) dB_dBnmtr() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) db_partition_from_options() (in module pyrosetta.rosetta.basic.database) dBR_dG() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) DbTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) DbTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) DC (class in pyrosetta.rosetta.core.scoring) DCcomputed() (pyrosetta.rosetta.core.scoring.DC method) DCerr() (pyrosetta.rosetta.core.scoring.DC method) Dconst() (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) DCval() (pyrosetta.rosetta.core.scoring.DC method) dD_dv1() (in module pyrosetta.rosetta.protocols.pockets) dD_dv2() (in module pyrosetta.rosetta.protocols.pockets) dD_dv3() (in module pyrosetta.rosetta.protocols.pockets) dD_dv4() (in module pyrosetta.rosetta.protocols.pockets) dD_dv5() (in module pyrosetta.rosetta.protocols.pockets) dD_dv6() (in module pyrosetta.rosetta.protocols.pockets) ddG_main() (in module pyrosetta.rosetta.protocols) DdGFeaturesCreator (class in pyrosetta.rosetta.protocols.features) deactivate() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) deallocate_arraypoolelement() (pyrosetta.rosetta.core.scoring.EnergyGraph method) debug() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) debug_dump_icoor() (pyrosetta.rosetta.core.chemical.ResidueType method) debug_dump_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) debug_pause() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) debug_residue_torsions() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) decide_is_d_aa() (pyrosetta.rosetta.core.io.NomenclatureManager method) decide_is_known_achiral() (pyrosetta.rosetta.core.io.NomenclatureManager method) decide_is_l_aa() (pyrosetta.rosetta.core.io.NomenclatureManager method) decide_read_from_binary() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) decide_to_keep_pose() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) declare_chemical_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) declare_chemical_bonds_at_cutpoints() (in module pyrosetta.rosetta.protocols.stepwise.modeler) declare_cutpoint_chemical_bond() (in module pyrosetta.rosetta.core.pose) declare_minimization_over() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) DeclareStructureDataCovalentBondMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) decode6bit() (in module pyrosetta.rosetta.utility) decode_32_to_24() (in module pyrosetta.rosetta.utility) decompose() (in module pyrosetta.rosetta.protocols.nonlocal) decoy_compatibility() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) decoy_tag() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) decoys() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) decoys_returned() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) decrease_double_lazy_ig_memlimit() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) decrease_linmem_ig_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) decreasing() (pyrosetta.rosetta.protocols.loops.Loop method) decrement_from_cached() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) decrement_reference_pose_mapping_after_seqpos() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) def() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) default_active() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) default_filename() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) default_inactive() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) default_jump_atom() (in module pyrosetta.rosetta.core.chemical.rna) default_movemap_factory_attribute_name() (in module pyrosetta.rosetta.core.select.movemap) default_options() (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) default_position_from_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) default_rts() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) default_score_function() (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) default_size() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) default_stereochem_from_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) default_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) default_to() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) default_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) DefaultCubeHash (class in pyrosetta.rosetta.core.conformation) define_architect_group() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) define_chains() (in module pyrosetta.rosetta.core.import_pose) define_composition_schema() (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) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) define_features_reporter_xml_schema_group() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) define_loop_definer_xml_schema() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) define_loops() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) define_mainchain_atoms() (in module pyrosetta.rosetta.core.chemical) define_mg_water_map() (in module pyrosetta.rosetta.protocols.magnesium) define_pairing_group() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) define_rdf_function_group() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) define_scorable_core_from_secondary_structure() (in module pyrosetta.rosetta.protocols.loops) define_start_window() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) define_valid_filter_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) define_valid_perturber_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) define_valid_selector_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) defined_adducts() (pyrosetta.rosetta.core.chemical.ResidueType method) defined_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) defines_custom_rama_prepro_map() (pyrosetta.rosetta.core.chemical.ResidueType method) defines_dof_derivatives() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) defines_high_order_terms() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) defines_intrares_dof_derivatives() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) defines_intrares_energy() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) defines_intrares_energy_for_residue() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) defines_residue_pair_energy() (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) defines_score_for_residue() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) defines_score_for_residue_pair() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) definite_terminal_root() (in module pyrosetta.rosetta.core.pose) defs2map() (in module pyrosetta.rosetta.protocols.motifs) defs2vector() (in module pyrosetta.rosetta.protocols.motifs) degrees() (in module pyrosetta.rosetta.numeric.conversions) delete_act_coord_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_all_intragroup_edges() (in module pyrosetta.rosetta.utility.graph) delete_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) delete_atom_alias() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_carbohydrate_branch() (in module pyrosetta.rosetta.core.pose.carbohydrates) delete_chain_ending() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) delete_child_proton() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_comment() (in module pyrosetta.rosetta.core.pose) delete_contents_at_nread_limit() (pyrosetta.rosetta.utility.io.FileContentsMap method) delete_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) delete_extra_vertices() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) delete_jump_and_intervening_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_leaf() (in module pyrosetta.rosetta.core.pose.carbohydrates) delete_loop() (pyrosetta.rosetta.protocols.loops.Loops method) delete_lower_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) delete_metalbinding_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_non_protein_from_pose() (in module pyrosetta.rosetta.protocols.rna.denovo) delete_overhang_residues() (in module pyrosetta.rosetta.protocols.grafting) delete_polymer_residue() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) delete_pose() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) delete_property() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_record() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) delete_region() (in module pyrosetta.rosetta.protocols.grafting) delete_res() (pyrosetta.rosetta.core.pose.PDBInfo method) delete_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) delete_residue_range_slow() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) delete_residue_slow() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) delete_segment() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_segments() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) delete_self_edges() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_seqpos() (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_source_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) delete_submotif_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) delete_target_residue() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) delete_terminal_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) delete_this_struct_id() (in module pyrosetta.rosetta.protocols.features.strand_assembly) delete_this_sw_can_by_sh_id_from_sw_by_comp() (in module pyrosetta.rosetta.protocols.features.strand_assembly) delete_unordered_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_upper_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) delete_virtual_residues() (in module pyrosetta.rosetta.protocols.relax) DeleteActCoordAtom (class in pyrosetta.rosetta.core.chemical) DeleteAllRotamerSetOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) DeleteAtom (class in pyrosetta.rosetta.core.chemical) DeleteChainsMover (class in pyrosetta.rosetta.protocols.simple_moves) DeleteChildProton (class in pyrosetta.rosetta.core.chemical) DeleteMetalbindingAtom (class in pyrosetta.rosetta.core.chemical) DeleteMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) DeleteProperty (class in pyrosetta.rosetta.core.chemical) DeleteRegionMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) deletes_atom() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) deletes_atoms() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) deletes_properties() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) deletes_property() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) deletes_variant() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) deletes_variants() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) DeleteTerminalChi (class in pyrosetta.rosetta.core.chemical) DeleteVariantType (class in pyrosetta.rosetta.core.chemical) delta() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) delta_cutoff() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) delta_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) delta_omega0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_omega1_all() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_omega1_vect() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) delta_t() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_z1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) delta_z1_vect() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) deltaG_bind() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) denom() (in module pyrosetta.rosetta.protocols.cryst) DeNovoArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) DeNovoArchitectFactory (class in pyrosetta.rosetta.protocols.denovo_design.architects) DeNovoMotifArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) DenseEnergyContainer (class in pyrosetta.rosetta.core.scoring) DenseNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) DenseNeighborIterator (class in pyrosetta.rosetta.core.scoring) DensitySymmInfo (class in pyrosetta.rosetta.protocols.electron_density) DenyPdbIdFilter (class in pyrosetta.rosetta.protocols.frag_picker) 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) dependencies_exist() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) dependent_begin() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) dependent_end() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) dependent_on() (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) depends_on_polymer_lower() (pyrosetta.rosetta.core.chemical.AtomICoor method) depends_on_polymer_upper() (pyrosetta.rosetta.core.chemical.AtomICoor method) depends_on_residue_connection() (pyrosetta.rosetta.core.chemical.AtomICoor method) deposition_date() (pyrosetta.rosetta.core.io.HeaderInformation method) deprecated_eval_atom_derivative() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) depth() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) deriv_check() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) deriv_check_result() (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) deriv_score() (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) derivative_atom() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) derivatives() (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) derive_from_src_lib() (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) derive_peptide() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) derive_sc_sc_restraints() (in module pyrosetta.rosetta.protocols.relax) derived_dofs() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) DerivedSequenceMapping (class in pyrosetta.rosetta.core.sequence) DerivVectorPair (class in pyrosetta.rosetta.core.scoring) describe_fragments() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) describe_score() (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) description() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) deserialize() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) deserialize_db_listener_data() (in module pyrosetta.rosetta.protocols.features) deserialize_xyz_coords() (in module pyrosetta.rosetta.protocols.features) design() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) design_all_aas() (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) design_antigen() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) design_any() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) design_chain1() (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) design_chain2() (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) design_framework() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) design_loop() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) design_neighbors() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) design_only_target_residues() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) design_proline() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) design_protocol_to_enum() (in module pyrosetta.rosetta.protocols.antibody.design) design_protocol_to_string() (in module pyrosetta.rosetta.protocols.antibody.design) design_residue() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) designable() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) DesignContrast (class in pyrosetta.rosetta.core.io.sequence_comparation) designing_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) DesignMeanField (class in pyrosetta.rosetta.protocols.mean_field) DesignMinimizeHbonds (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DesignRepackMover (class in pyrosetta.rosetta.protocols.simple_moves) DesignTask (class in pyrosetta.rosetta.protocols.flxbb) DesignTask_Layer (class in pyrosetta.rosetta.protocols.flxbb) DesignTask_Normal (class in pyrosetta.rosetta.protocols.flxbb) DesignVsNativeComparison (class in pyrosetta.rosetta.protocols.enzdes) desired_ala_fraction() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) desired_loops() (pyrosetta.rosetta.protocols.LoopRebuild method) desired_min_hydrophobic_fraction() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) desired_remodelres_in_vicinity() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) desired_result() (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) destination_size() (pyrosetta.rosetta.utility.subset_mapping method) destructed() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) DestructionEvent (class in pyrosetta.rosetta.core.pose.signals) desymmeterize() (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) desymmeterize_upstream_restype_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) det3() (in module pyrosetta.rosetta.numeric.model_quality) detach() (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) detach_after_modify() (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) detach_from() (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (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) detach_from_conformation() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) detach_impl() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) detach_observer() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) detached_clone() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) detached_copy() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) detect() (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) detect_axes() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) detect_base_contacts() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge) detect_bonds() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) detect_disulfides() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) detect_heavy_chain() (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) detect_ld_chirality_from_polymer_residue() (in module pyrosetta.rosetta.core.chemical) detect_light_chain() (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) detect_phosphate_contacts() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) detect_pseudobonds() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) detect_sugar_contacts() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) DetectProteinLigandInterface (class in pyrosetta.rosetta.protocols.enzdes) determine_atom_inds_for_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) determine_core_heading_surface_heading_by_distance() (in module pyrosetta.rosetta.protocols.features.strand_assembly) determine_cyclization_viability() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) determine_file_type() (in module pyrosetta.rosetta.core.import_pose) determine_heading_direction_by_vector() (in module pyrosetta.rosetta.protocols.features.strand_assembly) determine_largest_nbr_atom_distance() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) determine_lo_and_hi_residues() (in module pyrosetta.rosetta.core.scoring.methods) determine_loop() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) determine_random_number_seed() (in module pyrosetta.rosetta.core.init) determine_redundant_upstream_matchres() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) determine_score_variations() (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) dEtot_dEhb() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) deviation() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) dexponential() (in module pyrosetta.rosetta.core.scoring.constraints) dfour1_plan() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) dfs() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) dfunc() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) dfunc_component() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) dG_dCi() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) dgaussian() (in module pyrosetta.rosetta.core.scoring.constraints) DGBindOptEData (class in pyrosetta.rosetta.protocols.optimize_weights) Di() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) DiagnosticData (class in pyrosetta.rosetta.basic.datacache) difference_from() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) differentiate() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) Digraph (class in pyrosetta.rosetta.utility.graph) digraph_is_a_DAG() (in module pyrosetta.rosetta.utility.graph) dihedral() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) dihedral_between_bonded_children() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) dihedral_degrees() (in module pyrosetta.rosetta.numeric) dihedral_degrees_double() (in module pyrosetta.rosetta.numeric) dihedral_diff() (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) dihedral_distance() (in module pyrosetta.rosetta.protocols.idealize) dihedral_double() (in module pyrosetta.rosetta.numeric) dihedral_radians() (in module pyrosetta.rosetta.numeric) dihedral_radians_double() (in module pyrosetta.rosetta.numeric) dihedral_rmsd() (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) DihedralConstraint (class in pyrosetta.rosetta.core.scoring.constraints) DihedralConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints)

DihedralConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) DihedralPairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) DihedralPairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) dihedrals_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) dijkstras() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) dim() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dim_labels() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) Dimension (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpression (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionCon (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionCube (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionDiv (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionMax (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionMin (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionMul (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionPow (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionRef (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionSquare (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionSub (class in pyrosetta.rosetta.ObjexxFCL) DimensionExpressionSum (class in pyrosetta.rosetta.ObjexxFCL) dimOther() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) dimprod() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) dimReal() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) dims() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) dims_v() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) dimsizes() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) DipolarCoupling (class in pyrosetta.rosetta.core.scoring) dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) dir() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) DirectedEdgeList (class in pyrosetta.rosetta.utility.graph) DirectedEdgeListConstIterator (class in pyrosetta.rosetta.utility.graph) DirectedEdgeListElement (class in pyrosetta.rosetta.utility.graph) DirectedEdgeListIterator (class in pyrosetta.rosetta.utility.graph) Direction (class in pyrosetta.rosetta.protocols.rigid) direction() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) directory() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) DirectReadoutEnergy (class in pyrosetta.rosetta.core.scoring.methods) DirectReadoutPotential (class in pyrosetta.rosetta.core.scoring.dna) dis() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) disable() (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) disable_auto_update() (pyrosetta.rosetta.core.scoring.NeighborList method) disable_autotemp() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) disable_build_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) disable_centroid_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) disable_cis_pro_sampling() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) disable_conserved_framework_positions() (in module pyrosetta.rosetta.protocols.antibody.design) disable_constraint_scoreterms() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) disable_design_antigen() (in module pyrosetta.rosetta.protocols.antibody.design) disable_design_cdr() (in module pyrosetta.rosetta.protocols.antibody.design) disable_design_cdrs() (in module pyrosetta.rosetta.protocols.antibody.design) disable_design_for_non_designing_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) disable_design_framework() (in module pyrosetta.rosetta.protocols.antibody.design) disable_design_region() (in module pyrosetta.rosetta.protocols.antibody.design) disable_disallowed_aa() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) disable_fullatom_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) disable_h3_stem_positions() (in module pyrosetta.rosetta.protocols.antibody.design) disable_ignorefinished() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) disable_inprogress() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) disable_output() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) disable_proline_design() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) disable_sampling_of_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) disable_total_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) DisableAntibodyRegionOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) DisableCDRsOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) disallow_aas() (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) disallow_movement_of_input_res() (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) disallow_noncanonical_aas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) disallow_pack_polar_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) disallow_quench() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) disallow_realign() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) disallow_resid() (pyrosetta.rosetta.core.pack.task.operation.OptH method) DisallowIfNonnative (class in pyrosetta.rosetta.core.pack.task.operation) discard_conformation_domain_map() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) disconnected_segments() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) discontinued_lower() (in module pyrosetta.rosetta.protocols.hybridization) discontinued_upper() (in module pyrosetta.rosetta.protocols.hybridization) DiscreteRandomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) DisembodiedAssembly (class in pyrosetta.rosetta.protocols.sewing) dist() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) dist_cutoff() (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) dist_square() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) distance() (in module pyrosetta.rosetta.core.kinematics) (in module pyrosetta.rosetta.core.kinematics.tree) (in module pyrosetta.rosetta.protocols.mpi_refinement) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) distance_cutoff() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) distance_diff() (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) distance_from_line2D() (in module pyrosetta.rosetta.core.membrane) distance_pair() (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) distance_squared() (in module pyrosetta.rosetta.core.kinematics.tree) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) distance_squared_cb() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) distance_squared_cen() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) DistanceChainbreakEnergy (class in pyrosetta.rosetta.core.scoring.methods) DistanceConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) DistancePairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) DistanceResidueNetwork (class in pyrosetta.rosetta.protocols.toolbox) DistanceScoreMover (class in pyrosetta.rosetta.protocols.noesy_assign) distbin_map() (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) distinguish_backbone_and_sidechain_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) distinguish_pucker() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) DistributionMap (class in pyrosetta.rosetta.protocols.ligand_docking) disulf_atom_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) disulfide_bonds() (in module pyrosetta.rosetta.core.conformation) DisulfideAtomIndices (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) DisulfideFile (class in pyrosetta.rosetta.core.io.raw_data) DisulfideFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) DisulfideIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) DisulfideInsertionMover (class in pyrosetta.rosetta.protocols.simple_moves) DisulfideMatchingEnergyComponents (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingNeighborConstIterator (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingNeighborIterator (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingPotential (class in pyrosetta.rosetta.core.scoring.disulfides) disulfides() (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) DisulfJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) diversify_all_confs() (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) DiversifyCrmsdByClustering (class in pyrosetta.rosetta.protocols.frag_picker) DiversifyCrmsdSelector (class in pyrosetta.rosetta.protocols.frag_picker) DiversifyDihedralsSelector (class in pyrosetta.rosetta.protocols.frag_picker) DiversifyStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) divide_and_conquer() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) DivideAndConqueror (class in pyrosetta.rosetta.protocols.denovo_design.components) divides_backbone_and_sidechain_energetics() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) dk() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) dljatr() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dljrep() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dna_base_partner() (in module pyrosetta.rosetta.protocols.dna) dna_comp_name_str() (in module pyrosetta.rosetta.protocols.dna) DNA_EnvPairEnergy (class in pyrosetta.rosetta.core.scoring.methods) dna_full_name3() (in module pyrosetta.rosetta.protocols.dna) DnaDesignDef (class in pyrosetta.rosetta.protocols.dna) DnaInterfaceMultiStateDesign (class in pyrosetta.rosetta.protocols.dna) dncase() (in module pyrosetta.rosetta.ObjexxFCL) dnmtr() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) do_apply() (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) do_caching() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) do_caching_simple() (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) do_correct_NH() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) do_distributed_rerun() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) do_final_fastrelax() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) do_final_repack() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) do_I_skip() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) do_not_autoassign_SS() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) do_not_sample_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) do_one_line() (in module pyrosetta.rosetta.protocols.frag_picker.scores) do_packing() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) do_prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) do_recursion() (in module pyrosetta.rosetta.numeric.random) do_rerun() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) do_score() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) do_scoring() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) do_set_xyz() (in module pyrosetta.rosetta.protocols.stepwise.sampler.protein) do_xy_scan() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) dock_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) dock_high_res() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) dock_low_res() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) docking_highres_filter() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) docking_highres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) docking_lowres_filter() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) docking_lowres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) DockingEnsemble (class in pyrosetta.rosetta.protocols.docking) DockingHighResFactory (class in pyrosetta.rosetta.protocols.docking) DockingHighResFilter (class in pyrosetta.rosetta.protocols.docking) DockingHighResLegacy (class in pyrosetta.rosetta.protocols.docking) DockingInitialPerturbation (class in pyrosetta.rosetta.protocols.docking) DockingLowResFilter (class in pyrosetta.rosetta.protocols.docking) DockingProtocol (class in pyrosetta.rosetta.protocols.docking) DockingSlideIntoContact (class in pyrosetta.rosetta.protocols.docking) DockIntoDensityMover (class in pyrosetta.rosetta.protocols.electron_density) dockPoseIntoMap() (in module pyrosetta.rosetta.protocols.electron_density) DockSetupMover (class in pyrosetta.rosetta.protocols.docking) DockWithHotspotMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) dof() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) DOF_bin_size() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) DOF_bin_value() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) DOF_Constraint (class in pyrosetta.rosetta.core.scoring.constraints) dof_deriv_1benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) dof_deriv_1benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) dof_deriv_2benmeths_begin() (pyrosetta.rosetta.core.scoring.MinimizationNode method) dof_deriv_2benmeths_end() (pyrosetta.rosetta.core.scoring.MinimizationNode method) DoF_helix_index() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) DOF_ID (class in pyrosetta.rosetta.core.id) dof_id() (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) dof_id_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) dof_id_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) dof_id_from_atom_ids() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) dof_id_from_torsion_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) DOF_ID_Range (class in pyrosetta.rosetta.core.id) DoF_name() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) dof_node_from_id() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) dof_nodes() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) DoF_sample_value() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) DOF_Type (class in pyrosetta.rosetta.core.id) DoF_type() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) dof_type_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) dof_type_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) DOF_type_is_rb() (in module pyrosetta.rosetta.core.id) dofs() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) dofs_to_vars() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) DoFType (class in pyrosetta.rosetta.protocols.helical_bundle) domain_map() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) DomainAssembly (class in pyrosetta.rosetta.protocols.abinitio) don_bbg_in_bb_bb_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) donor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) dont_be_lenient() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) dont_check_overlap() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) dont_check_rama() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) dot() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.numeric.kinematic_closure) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) dot_abs() (pyrosetta.rosetta.core.scoring.EnergyEdge method) dot_coord() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) dot_exposed() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) DotSphere (class in pyrosetta.rosetta.core.pack.interaction_graph) double_lazy_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) double_lazy_ig_memlimit() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) double_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) DoubleLazyInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) down_cast() (in module pyrosetta.rosetta.utility) downstream() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) downstream_atom() (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) downstream_builder() (pyrosetta.rosetta.protocols.match.Matcher method) downstream_builders() (pyrosetta.rosetta.protocols.match.Matcher method) downstream_centroid_by_jump() (in module pyrosetta.rosetta.protocols.geometry) downstream_combine() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) downstream_jump_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) downstream_jump_stub() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) downstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) downstream_residues_from_jump() (in module pyrosetta.rosetta.protocols.hybridization) DownstreamAlgorithm (class in pyrosetta.rosetta.protocols.match.downstream) DownstreamRMSEvaluator (class in pyrosetta.rosetta.protocols.match.output) drift() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) drop_all_edges() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) drop_all_edges_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) drop_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) drop_edge() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) drop_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) drop_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) drop_rotamers_by_index() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) drop_strand_pairs() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) drop_unsatisfied_voxels() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) dround() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) dry_run() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) ds_hitset_end_its() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) ds_hitset_its() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) dSA_dDi() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) dscore() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) dslfc_ang() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_bb_dih() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cb_dih() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cb_dst() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cen_dst() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_rot() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) dslfc_RT() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) dslfc_trans() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) dsolv() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dsolv1() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dsolv2() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) dsolv_dBR() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) Dssp (class in pyrosetta.rosetta.core.scoring.dssp) dssp() (in module pyrosetta.rosetta.protocols.simple_filters) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_featurizer() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_phi() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) dssp_psi() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) dssp_reduced() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_reduced_IG_as_L() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_reduced_IG_as_L_if_adjcent_H() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) dssp_state() (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) DsspDesignOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) DualMonteCarlo (class in pyrosetta.rosetta.protocols.moves) dummy_modify() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) dump() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) dump_as_pdb() (in module pyrosetta.rosetta.protocols.toolbox) dump_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_cif() (in module pyrosetta.rosetta.core.io.mmcif) (pyrosetta.rosetta.core.pose.Pose method) dump_comment_pdb() (in module pyrosetta.rosetta.core.pose) dump_cst_file() (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) dump_eggshell() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) dump_file() (pyrosetta.rosetta.core.pose.Pose method) dump_frames_as_pdb() (in module pyrosetta.rosetta.core.fragment) dump_gws() (in module pyrosetta.rosetta.core.io.carbohydrates) dump_gws_chain() (in module pyrosetta.rosetta.core.io.carbohydrates) dump_invrots_tree_as_multimodel_pdbs() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) dump_loophash_linkers() (in module pyrosetta.rosetta.protocols.sic_dock) dump_packertask() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) dump_pdb() (in module pyrosetta.rosetta.core.io.pdb) (pyrosetta.rosetta.core.pose.Pose method) dump_pdb_residue() (in module pyrosetta.rosetta.core.io.pdb) dump_points_pdb() (in module pyrosetta.rosetta.protocols.sic_dock) dump_pose() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) dump_pose_and_map() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) dump_pose_kinemage() (in module pyrosetta.rosetta.protocols.viewer) dump_reference_pose() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_score_line() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_scored_pdb() (pyrosetta.rosetta.core.pose.Pose method) dump_silent() (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) dump_vall_fasta() (in module pyrosetta.rosetta.protocols.frags) dump_vd_info() (pyrosetta.rosetta.core.chemical.ResidueType method) dump_weights() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) dumpExemplarToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dumpGridToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) DumpPdb (class in pyrosetta.rosetta.protocols.simple_moves) DumpSingleResidueRotamers (class in pyrosetta.rosetta.protocols.simple_moves) dumpTargetPocketsToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dumpTargetPocketsToPDB() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dunbrack_print() (in module pyrosetta.rosetta.protocols.make_rot_lib) DunbrackAAParameterSet (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackConstraintCreator (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackSCSampler (class in pyrosetta.rosetta.protocols.match.upstream) dweight() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) dx_ddelta_omega1() (in module pyrosetta.rosetta.numeric.crick_equations) dx_ddelta_z1() (in module pyrosetta.rosetta.numeric.crick_equations) dx_ddz1() (in module pyrosetta.rosetta.numeric.crick_equations) dx_domega1() (in module pyrosetta.rosetta.numeric.crick_equations) dx_dr1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_ddelta_omega1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_ddelta_z1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_ddz1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_domega1() (in module pyrosetta.rosetta.numeric.crick_equations) dy_dr1() (in module pyrosetta.rosetta.numeric.crick_equations) dynamic_memory_usage() (pyrosetta.rosetta.utility.recent_history_queue method) DynamicIndexRange (class in pyrosetta.rosetta.ObjexxFCL) dz_ddelta_omega1() (in module pyrosetta.rosetta.numeric.crick_equations) dz_ddelta_z1() (in module pyrosetta.rosetta.numeric.crick_equations) dz_ddz1() (in module pyrosetta.rosetta.numeric.crick_equations) dz_domega1() (in module pyrosetta.rosetta.numeric.crick_equations) dz_dr1() (in module pyrosetta.rosetta.numeric.crick_equations)