Index – D

D (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon property) d() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) d1() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) d2 (pyrosetta.rosetta.protocols.normalmode.ContactStruct property) d2() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) d2h_sa (pyrosetta.rosetta.core.scoring.ScoreType attribute) D2H_SA_Energy (class in pyrosetta.rosetta.core.energy_methods) D2H_SA_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) d2s() (pyrosetta.rosetta.utility.subset_mapping method) D_AA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) d_array_scale() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) D_CHIRALITY (pyrosetta.rosetta.protocols.simple_moves.chiral.Chirality attribute) d_hbond_weight_dE() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) d_ind() (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) d_location (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) d_phi() (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) d_psi() (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) D_RNA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) d_scale (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) d_shape (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) D_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) dab_sasa (pyrosetta.rosetta.core.scoring.ScoreType attribute) DAB_SASA_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) dab_sev (pyrosetta.rosetta.core.scoring.ScoreType attribute) DAB_SEV_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) dada (pyrosetta.rosetta.core.scoring.packstat.Circle property) daemon_set() (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction method) daemons() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) DaemonSet (class in pyrosetta.rosetta.protocols.pack_daemon) DaemonSetMessage (class in pyrosetta.rosetta.protocols.pack_daemon) DALPHABALL (pyrosetta.rosetta.basic.ProfTag attribute) DALPHABALL_DERIV (pyrosetta.rosetta.basic.ProfTag attribute) dangling_res() (pyrosetta.rosetta.protocols.recces.params.RECCES_Parameters method) DarcParticleSwarmMinimizer (class in pyrosetta.rosetta.protocols.pockets) DATA (pyrosetta.rosetta.protocols.sparta.GDB property) data() (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet 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) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) (pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) data_annotations() (pyrosetta.rosetta.core.io.rna.RDAT method) data_dim() (in module pyrosetta.rosetta.protocols.recces) data_int() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) data_integrity_check() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) data_line (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData property) data_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.DataLoaderFactory static method) data_map (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.ParsedTagCache property) data_ptr() (pyrosetta.rosetta.core.conformation.Residue method) data_real() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) DATA_STORAGE (pyrosetta.rosetta.basic.ProfTag attribute) data_str() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) data_type (pyrosetta.rosetta.protocols.features.MetricData property) DATABASE (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) database_dir() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) database_directory() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) database_entry() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) database_fname() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) database_mode_from_name() (in module pyrosetta.rosetta.utility.sql_database) database_pdb_entry() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) DATABASE_PROTOCOL_AND_BATCH_ID_TAG (pyrosetta.rosetta.basic.mpi.listener_tags attribute) database_session_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader static method) database_table() (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) DatabaseEntryWorkUnit (class in pyrosetta.rosetta.protocols.wum) DatabaseEntryWorkUnit.WU_Header (class in pyrosetta.rosetta.protocols.wum) DatabaseFilter (class in pyrosetta.rosetta.protocols.features) DatabaseJobInputter (class in pyrosetta.rosetta.protocols.features) DatabaseJobInputterCreator (class in pyrosetta.rosetta.protocols.features) DatabaseJobOutputter (class in pyrosetta.rosetta.protocols.features) DatabaseJobOutputterCreator (class in pyrosetta.rosetta.protocols.features) DatabaseMode (class in pyrosetta.rosetta.utility.sql_database) DatabaseMode.e (class in pyrosetta.rosetta.utility.sql_database) DatabaseOccSolEne (class in pyrosetta.rosetta.core.scoring.geometric_solvation) DatabaseRelaxScript (class in pyrosetta.rosetta.protocols.relax) DatabaseResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) DatabaseResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) DatabaseSessionLoader (class in pyrosetta.rosetta.protocols.parser) DatabaseSessionLoaderCreator (class in pyrosetta.rosetta.protocols.parser) DatabaseSessionManager (class in pyrosetta.rosetta.utility.sql_database) DatabaseThread (class in pyrosetta.rosetta.protocols.task_operations) DatabaseThreadCreator (class in pyrosetta.rosetta.protocols.task_operations) DataBuffer (class in pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) DataCache_basic_datacache_CacheableData_t (class in pyrosetta.rosetta.basic.datacache) DataCache_CacheableData (class in pyrosetta.rosetta.basic.datacache) DataCache_core_pose_datacache_CacheableObserver_t (class in pyrosetta.rosetta.basic.datacache) 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) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.environment.AutoCutData method) date() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.utility.Version static method) DateFormat (class in pyrosetta.rosetta.utility) Dawson() (in module pyrosetta.rosetta.numeric.statistics) Db (pyrosetta.rosetta.core.chemical.element.Elements attribute) dB_dBdnmtr() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) dB_dBdnmtr_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) dB_dBnmtr() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) dB_dBnmtr_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) db_entry() (pyrosetta.rosetta.protocols.splice.RBInMover method) DB_FNAME_LEVEL1_1 (pyrosetta.rosetta.protocols.sparta.ANN property) DB_FNAME_LEVEL1_2 (pyrosetta.rosetta.protocols.sparta.ANN property) DB_FNAME_LEVEL1_3 (pyrosetta.rosetta.protocols.sparta.ANN property) DB_FNAME_LEVEL2_1 (pyrosetta.rosetta.protocols.sparta.ANN property) DB_FNAME_LEVEL2_2 (pyrosetta.rosetta.protocols.sparta.ANN property) DB_FNAME_LEVEL2_3 (pyrosetta.rosetta.protocols.sparta.ANN property) DB_NAME_PREFIX (pyrosetta.rosetta.protocols.sparta.ANN property) db_partition_from_options() (in module pyrosetta.rosetta.basic.database) DB_PATH (pyrosetta.rosetta.protocols.sparta.ANN property) db_session() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) dbase_file_name() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) dbase_iterate() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) DbBigInt (class in pyrosetta.rosetta.basic.database.schema_generator) DbDataType (class in pyrosetta.rosetta.basic.database.schema_generator) DbDouble (class in pyrosetta.rosetta.basic.database.schema_generator) dbg (pyrosetta.rosetta.core.scoring.APBSConfig property) DbInteger (class in pyrosetta.rosetta.basic.database.schema_generator) DbMoverMessageListener (class in pyrosetta.rosetta.basic.mpi) dBR_dG() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) dBR_dG_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) DbReal (class in pyrosetta.rosetta.basic.database.schema_generator) DBREF (pyrosetta.rosetta.core.io.pdb.RecordType attribute) DBREF1 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) DBREF2 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) DbText (class in pyrosetta.rosetta.basic.database.schema_generator) DbTextKey (class in pyrosetta.rosetta.basic.database.schema_generator) DbTrajectoryReader (class in pyrosetta.rosetta.protocols.trajectory) DbTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) DbTrajectoryRecorder.Frame (class in pyrosetta.rosetta.protocols.canonical_sampling) DbTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) DbTrajectoryWriter (class in pyrosetta.rosetta.protocols.trajectory) DbTrajectoryWriter.Frame (class in pyrosetta.rosetta.protocols.trajectory) DbUUID (class in pyrosetta.rosetta.basic.database.schema_generator) dbx (pyrosetta.rosetta.core.scoring.APBSResult property) dby (pyrosetta.rosetta.core.scoring.APBSResult property) dbz (pyrosetta.rosetta.core.scoring.APBSResult property) DC (class in pyrosetta.rosetta.core.scoring) dc (pyrosetta.rosetta.core.scoring.ScoreType attribute) DC.DC_TYPE (class in pyrosetta.rosetta.core.scoring) DC_TYPE_CC (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DC.DC_TYPE attribute) DC_TYPE_CH (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DC.DC_TYPE attribute) DC_TYPE_NC (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DC.DC_TYPE attribute) DC_TYPE_NH (pyrosetta.rosetta.core.scoring.DC attribute) (pyrosetta.rosetta.core.scoring.DC.DC_TYPE attribute) dcalibrate_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) dCCdB_fastRes() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) dCCdBs() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) dCCdx_aacen() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) dCCdx_cen() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) dCCdx_fastRes() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) dCCdx_PointFast() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) dCCdx_res() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) DCcomputed() (pyrosetta.rosetta.core.scoring.DC method) DCerr() (pyrosetta.rosetta.core.scoring.DC method) dchidevpen_dbb() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dchidevpen_dchi() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dchimean_dbb() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dchimean_domg() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dchisd_dbb() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dchisd_domg() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) Dconst() (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.RDC method) dcs_kappa1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcs_kappa2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcs_kappa3 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcs_logA1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcs_logA2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcs_logA3 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcs_mu1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcs_mu2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcs_mu3 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dcut_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) DCV_ALREADY_CYCLIZED (pyrosetta.rosetta.protocols.simple_moves.DisulfideCyclizationViability attribute) DCV_CYCLIZABLE (pyrosetta.rosetta.protocols.simple_moves.DisulfideCyclizationViability attribute) DCV_NOT_CYCLIZABLE (pyrosetta.rosetta.protocols.simple_moves.DisulfideCyclizationViability attribute) DCval() (pyrosetta.rosetta.core.scoring.DC method) DCval_computed_ (pyrosetta.rosetta.core.scoring.DC property) 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 (class in pyrosetta.rosetta.protocols.simple_ddg) ddg (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk property) ddG() (pyrosetta.rosetta.protocols.ddg.ddGMover method) ddg() (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) ddg_based() (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) ddG_bind_correlation (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) ddG_for_single_residue() (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) ddG_ins (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.mutt property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.mutt property) ddG_main() (in module pyrosetta.rosetta.protocols) ddG_mover() (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) ddG_mutation_correlation (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) ddG_mutation_correlation_with_unfolded_energy (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) ddG_threshold() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) DDGBindOptEData (class in pyrosetta.rosetta.protocols.optimize_weights) DDGBindOptEData.DDG_Bind_File_Index (class in pyrosetta.rosetta.protocols.optimize_weights) ddGCreator (class in pyrosetta.rosetta.protocols.simple_ddg) ddGData (class in pyrosetta.rosetta.protocols.ddG) DdGFeatures (class in pyrosetta.rosetta.protocols.features) DdGFeaturesCreator (class in pyrosetta.rosetta.protocols.features) DdgFilter (class in pyrosetta.rosetta.protocols.simple_ddg) DdgFilterCreator (class in pyrosetta.rosetta.protocols.simple_ddg) ddGMover (class in pyrosetta.rosetta.protocols.ddg) DDGMutationOptEData (class in pyrosetta.rosetta.protocols.optimize_weights) DdGScan (class in pyrosetta.rosetta.protocols.simple_ddg) DdGScanCreator (class in pyrosetta.rosetta.protocols.simple_ddg) dDist_dv1 (pyrosetta.rosetta.protocols.pockets.ray_distance_derivs property) dDist_dv2 (pyrosetta.rosetta.protocols.pockets.ray_distance_derivs property) dDist_dv3 (pyrosetta.rosetta.protocols.pockets.ray_distance_derivs property) dDist_dv4 (pyrosetta.rosetta.protocols.pockets.ray_distance_derivs property) dDist_dv5 (pyrosetta.rosetta.protocols.pockets.ray_distance_derivs property) dDist_dv6 (pyrosetta.rosetta.protocols.pockets.ray_distance_derivs property) DDomainParse (class in pyrosetta.rosetta.protocols.hybridization) dDome_dBase() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) dDome_dOther() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) dDome_dWater() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) DDPlookup (class in pyrosetta.rosetta.core.scoring.interface_) DDPscore (class in pyrosetta.rosetta.core.scoring.interface_) DDPscoreCreator (class in pyrosetta.rosetta.core.scoring.interface_) ddy() (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) dE_dbb() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dE_dbb_dev() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dE_dbb_dev_perchi() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dE_dbb_rot() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dE_dbb_semi() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dE_dchi() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dE_dchi_dev() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dE_dchi_semi() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) de_novo_setup_from_command_line() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) de_novo_setup_from_options() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) de_novo_setup_from_tag() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) deactivate() (pyrosetta.rosetta.utility.Bound_bool_t method) (pyrosetta.rosetta.utility.Bound_double_t method) (pyrosetta.rosetta.utility.Bound_int_t method) (pyrosetta.rosetta.utility.Bound_std_string_t method) (pyrosetta.rosetta.utility.Bound_utility_file_FileName_t method) (pyrosetta.rosetta.utility.Bound_utility_file_PathName_t 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.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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) deallocate_array() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) deallocate_arraypoolelement() (pyrosetta.rosetta.core.scoring.EnergyGraph method) deallocate_arrays() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) deallocate_resource() (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) deallocation_messages() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) deallocation_msg_type (class in pyrosetta.rosetta.protocols.jd3.deallocation) deallocation_type() (pyrosetta.rosetta.protocols.jd3.deallocation.DeallocationMessage method) (pyrosetta.rosetta.protocols.jd3.deallocation.InputPoseDeallocationMessage method) (pyrosetta.rosetta.protocols.jd3.deallocation.ResourceDeallocationMessage method) DeallocationMessage (class in pyrosetta.rosetta.protocols.jd3.deallocation) DEAMIDATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) Debug (pyrosetta.rosetta.basic.MemTracer property) (pyrosetta.rosetta.basic.MemTracerImpl property) (pyrosetta.rosetta.basic.Tracer property) (pyrosetta.rosetta.basic.TracerImpl property) debug() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) debug_deriv() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) debug_disable_count_pair_ (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy property) debug_dump_icoor() (pyrosetta.rosetta.core.chemical.ResidueType method) debug_dump_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) debug_note_accepted_substitution() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) debug_note_considered_substitution() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) debug_note_projected_deltaE_of_considered_substitution() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) debug_note_rejected_substitution() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) debug_output() (pyrosetta.rosetta.protocols.ddg.ddGMover method) debug_pause() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) debug_pdb() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) debug_pdbs() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) debug_print_addresses() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) debug_print_hierarchy() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) debug_print_size_per_level() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) debug_residue_torsions() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) DebuggingAnnealer (class in pyrosetta.rosetta.core.pack.annealer) debugMol() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) DebugOut_MpiFileBuffer (class in pyrosetta.rosetta.protocols.jd2) dec15_score (pyrosetta.rosetta.core.scoring.packing.HolesResult property) decide_is_d_aa() (pyrosetta.rosetta.core.io.NomenclatureManager static method) decide_is_known_achiral() (pyrosetta.rosetta.core.io.NomenclatureManager static method) decide_is_l_aa() (pyrosetta.rosetta.core.io.NomenclatureManager static 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_all_edge_energies_final() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) declare_all_rotamers_initialized() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) declare_chemical_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) declare_chemical_bonds_at_cutpoints() (in module pyrosetta.rosetta.protocols.stepwise.modeler) declare_covalent_bond() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) declare_cutpoint_chemical_bond() (in module pyrosetta.rosetta.core.pose) declare_edge_energies_final() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) declare_energies_final() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) declare_minimization_over() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) declare_remodelable() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) DeclareBond (class in pyrosetta.rosetta.protocols.simple_moves) DeclareBondCreator (class in pyrosetta.rosetta.protocols.simple_moves) DeclareStructureDataCovalentBondMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) DeclareStructureDataCovalentBondMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) decode6bit() (in module pyrosetta.rosetta.utility) decode_32_to_24() (in module pyrosetta.rosetta.utility) decompose_bb_hb_into_pair_energies() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) DecomposeAndReweightEnergiesCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) DecoratedNetworkState (class in pyrosetta.rosetta.protocols.hbnet) decoy_compatibility() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) decoy_score (pyrosetta.rosetta.core.scoring.packing.HolesResult property) decoy_tag() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) DecoyFileData (class in pyrosetta.rosetta.core.io.raw_data) DecoyFileData.const_iterator (class in pyrosetta.rosetta.core.io.raw_data) DecoyFileData.iterator (class in pyrosetta.rosetta.core.io.raw_data) decoys() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (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.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) decoys_returned() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) DecoySetEvaluation (class in pyrosetta.rosetta.protocols.toolbox) DecoyStruct (class in pyrosetta.rosetta.core.io.raw_data) 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_counts() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode 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) deep_clone() (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter method) deep_copy() (in module pyrosetta.rosetta.core.chemical) (in module pyrosetta.rosetta.core.chemical.rotamers) (in module pyrosetta.rosetta.core.kinematics) (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.core.scoring.bin_transitions) (in module pyrosetta.rosetta.core.scoring.hbonds) (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.numeric.interpolation.spline) (in module pyrosetta.rosetta.protocols.antibody) (in module pyrosetta.rosetta.protocols.antibody.design) (in module pyrosetta.rosetta.protocols.loops) deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t (class in pyrosetta.rosetta.utility) DeepCopyOP_const_core_kinematics_MoveMap_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_const_core_pose_Pose_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_const_core_scoring_bin_transitions_BinTransitionCalculator_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_const_protocols_antibody_AntibodyInfo_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_const_protocols_loops_Loops_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_core_chemical_AtomProperties_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_core_chemical_ResidueProperties_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_core_chemical_rotamers_RotamerLibrarySpecification_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_core_kinematics_MoveMap_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_core_pose_Pose_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_core_scoring_ScoreFunction_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_numeric_interpolation_spline_BicubicSpline_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_numeric_interpolation_spline_CubicSpline_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_numeric_interpolation_spline_PolycubicSplineBase_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_numeric_MathNTensorBase_double_t (class in pyrosetta.rosetta.utility.pointer) DeepCopyOP_protocols_loops_Loops_t (class in pyrosetta.rosetta.utility.pointer) deer_trace() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) deer_trace_intra() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) DEERChiSqMethod (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) DEERData (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) DEERDataCache (class in pyrosetta.rosetta.core.scoring.epr_deer) DEERDecayData (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) DEERDistanceBounds (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) DEERDistanceDistribution (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) DEEREnergy (class in pyrosetta.rosetta.core.energy_methods) DEEREnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DEERIO (class in pyrosetta.rosetta.core.scoring.epr_deer) DEERJaccardMethod (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) DEERJSMethod (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) DEERMiscMethod (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) DEEROptimizeCoordsMover (class in pyrosetta.rosetta.protocols.simple_moves) DEEROptimizeCoordsMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) DEEROverlapMethod (class in pyrosetta.rosetta.core.scoring.epr_deer.metrics) 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) Default (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) default_angle() (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector static method) default_calculator() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) default_calculator_cop() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) default_calculator_nonconst() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) default_commands() (pyrosetta.rosetta.core.pack.task.ResfileContents method) default_crick_params_file() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) default_dihedral() (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector static method) default_distance() (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector static method) default_exclude_consecutive() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover static method) default_filename() (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) default_flexibility() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) default_helix_length() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) default_jump_atom() (in module pyrosetta.rosetta.core.chemical.rna) default_label() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover static method) default_mainchain_connectivity() (pyrosetta.rosetta.core.io.StructFileRep method) default_mainchain_connectivity_from_pdb_code() (pyrosetta.rosetta.core.io.NomenclatureManager static method) default_master() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) default_max_distance() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover static method) default_merge_chains() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover static method) default_movemap_factory_attribute_name() (in module pyrosetta.rosetta.core.select.movemap) default_position (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow property) default_position_from_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) default_precision_ (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager property) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager property) default_repeats() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) default_residue_name() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) default_rts() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) default_score_function() (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder static method) default_selector() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) default_stereochem_from_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) DEFAULT_t (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) default_try_all_pairs() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover static method) default_value() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) default_value_for_cstid() (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter static method) default_value_for_init_option() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) default_value_for_is_cstE() (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter static method) default_value_for_lambda_memory() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) default_value_for_resnum() (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter static method) default_value_for_score_type() (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter static method) default_value_for_temperature() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) default_value_for_threshold() (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter static method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) default_value_for_tolerance() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) default_value_for_unbound() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) default_value_for_whole_pose() (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter static method) default_width_ (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager property) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager property) DefaultCubeHash (class in pyrosetta.rosetta.core.conformation) DefaultPackerPalette (class in pyrosetta.rosetta.core.pack.palette) DefaultPackerPaletteCreator (class in pyrosetta.rosetta.core.pack.palette) DefaultStyle (pyrosetta.rosetta.basic.citation_manager.CitationFormat attribute) defaultTestResult() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) define_active_site_from_gridlig_file() (pyrosetta.rosetta.protocols.match.MatcherTask method) define_active_site_from_residue_radii_list() (pyrosetta.rosetta.protocols.match.MatcherTask method) define_architect_group() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) define_assembly_mover_ct_gen() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover static method) define_assembly_requirement_subtag() (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementFactory method) define_assembly_scorer_subtag() (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerFactory method) define_chains() (in module pyrosetta.rosetta.core.import_pose) define_chemistry_xml_schema() (pyrosetta.rosetta.protocols.chemistries.ChemistryFactory method) define_chunk_library_inputter_xml_schema() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory method) define_cluster_metric_xml_schema() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory method) define_composition_schema() (pyrosetta.rosetta.core.pack.task.operation.AllResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition static method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover static method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover static method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer static method) define_constraint_generator_xml_schema_group() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory method) define_ddG_schema() (pyrosetta.rosetta.protocols.simple_ddg.ddG static method) define_envclaim_schema_group() (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim static method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim static method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim static method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim static method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim static method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim static method) define_explicit_water_mover_schema() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover static method) define_features_reporter_xml_schema_group() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) define_filter_xml_schema() (pyrosetta.rosetta.protocols.filters.FilterFactory method) define_full_model_inputter_xml_schema() (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory method) define_generic_assembly_mover_attributes() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover static method) define_global_requirements_subelement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) define_ideal_contacts_subelement() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer static method) define_intra_segment_requirements_subelement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) define_jump_selector_xml_schema() (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory method) define_local_frame() (in module pyrosetta.rosetta.core.scoring.nmr) define_loop_definer_xml_schema() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) define_loops() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) define_match_by_single_downstream_positioning() (pyrosetta.rosetta.protocols.match.MatcherTask method) define_mc_assembly_mover_ct_gen() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover static method) define_mg_water_map() (in module pyrosetta.rosetta.protocols.magnesium) define_mover_xml_schema() (pyrosetta.rosetta.protocols.moves.MoverFactory method) define_packer_palette_xml_schema() (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) define_pairing_group() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect static method) define_pose_inputter_xml_schema() (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory method) define_pose_outputter_xml_schema() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) define_pose_reporter_group() (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory method) define_pose_selector_group() (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory method) define_rdf_function_group() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) define_res_filter_xml_schema() (pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory method) define_res_lvl_task_op_xml_schema() (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) define_residue_selector_xml_schema() (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) define_scorable_core_from_secondary_structure() (in module pyrosetta.rosetta.protocols.loops) define_secondary_pose_outputter_xml_schema() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) define_simple_metric_xml_schema() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory method) define_start_window() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) define_task_op_xml_schema() (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) define_valid_filter_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter static method) define_valid_perturber_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber static method) define_valid_selector_name_enumeration() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector static method) defined() (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds method) (pyrosetta.rosetta.protocols.jumping.MembraneJump method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) defined_adducts() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase 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) defineEnergyMethodCreator() (in module pyrosetta) DefineMovableLoops (class in pyrosetta.rosetta.protocols.seeded_abinitio) DefineMovableLoopsCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) defines_custom_rama_prepro_map() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) defines_dof_derivatives() (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) defines_high_order_terms() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) defines_intrares_dof_derivatives() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) defines_intrares_energy() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) defines_intrares_energy_for_residue() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) defines_p_aa_pp_energy_for_res() (pyrosetta.rosetta.core.scoring.P_AA method) defines_residue_pair_energy() (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) defines_retry_limit() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) defines_score_for_residue() (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.Ramachandran method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) defines_score_for_residue_pair() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) definite_terminal_root() (in module pyrosetta.rosetta.core.pose) defs2BuildPositions() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) defs2BuildPositions_findts() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) defs2map() (in module pyrosetta.rosetta.protocols.motifs) defs2vector() (in module pyrosetta.rosetta.protocols.motifs) deg2rad() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) degeneracy (pyrosetta.rosetta.core.chemical.rings.RingConformer property) degree() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.numeric.Polynomial_1d method) DEGREES (pyrosetta.rosetta.numeric.conversions.AngleUnit attribute) degrees (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info property) degrees() (in module pyrosetta.rosetta.numeric.conversions) degrees_of_saturation() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) degrees_to_radians() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) del_ref() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.backend.driver method) (pyrosetta.rosetta.cppdb.backend.loadable_driver method) (pyrosetta.rosetta.cppdb.backend.result method) (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.pool method) (pyrosetta.rosetta.cppdb.ref_counted method) DELETE (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) delete_actcoord_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) delete_all_intragroup_edges() (in module pyrosetta.rosetta.utility.graph) delete_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType 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.MutableResidueType method) delete_bond() (pyrosetta.rosetta.core.chemical.MutableResidueType 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) delete_chi() (pyrosetta.rosetta.core.chemical.MutableResidueType method) delete_child_proton() (pyrosetta.rosetta.core.chemical.MutableResidueType method) delete_comment() (in module pyrosetta.rosetta.core.pose) delete_content_only() (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) delete_contents_at_nread_limit() (pyrosetta.rosetta.utility.io.FileContentsMap method) delete_data() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) delete_db() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) delete_diagonal_peaks() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) DELETE_DOWNSTREAM (pyrosetta.rosetta.protocols.indexed_structure_store.OverlapDeleteMode attribute) DELETE_EDGE (pyrosetta.rosetta.protocols.legacy_sewing.move_type attribute) delete_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) delete_edges_with_degree_zero() (in module pyrosetta.rosetta.core.pack.hbonds) delete_everything() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) delete_extra_vertices() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) delete_hairpin() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) delete_hairpin_c() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) delete_hairpin_n() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) delete_homologs() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) delete_interface_native_sidechains() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) delete_jump_and_intervening_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) delete_leading_residues() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) delete_leaf() (in module pyrosetta.rosetta.core.pose.carbohydrates) delete_loop() (pyrosetta.rosetta.protocols.loops.Loops method) DELETE_LOOP_RES (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) delete_lower_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) delete_metalbinding_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) delete_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) delete_non_protein_from_pose() (in module pyrosetta.rosetta.protocols.rna.denovo) delete_nu() (pyrosetta.rosetta.core.chemical.MutableResidueType method) 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) delete_pose() (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) delete_pose_from_tag() (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) delete_position() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) DELETE_PREVIOUS_ROTAMER (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelectorDecision attribute) delete_property() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) delete_record() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) 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.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) delete_residue_connection() (pyrosetta.rosetta.core.chemical.MutableResidueType 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) delete_ring() (pyrosetta.rosetta.core.chemical.MutableResidueType method) DELETE_ROTAMER (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelectorDecision attribute) delete_segment() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) delete_segment_basis_pairs() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) delete_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_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.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) delete_structure_store() (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager method) delete_submotif_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) delete_target_residue() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) delete_terminal_chi() (pyrosetta.rosetta.core.chemical.MutableResidueType 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_trailing_residues() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) delete_unordered_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) delete_upper_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) DELETE_UPSTREAM (pyrosetta.rosetta.protocols.indexed_structure_store.OverlapDeleteMode attribute) delete_virtual_residues() (in module pyrosetta.rosetta.protocols.relax) delete_waters() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) DeleteActCoordAtom (class in pyrosetta.rosetta.core.chemical) DeleteAllRotamerSetOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) DeleteAtom (class in pyrosetta.rosetta.core.chemical) DeleteBondOrder (pyrosetta.rosetta.core.chemical.BondOrder attribute) DeleteChainMover (class in pyrosetta.rosetta.protocols.simple_moves) DeleteChainMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) DeleteChainsMover (class in pyrosetta.rosetta.protocols.simple_moves) DeleteChainsMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) DeleteChildProton (class in pyrosetta.rosetta.core.chemical) deleted() (pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) DeleteMetalbindingAtom (class in pyrosetta.rosetta.core.chemical) DeleteMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) DeleteMoverCreator (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) DeleteRegionMoverCreator (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.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory 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.RenameAtom 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.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge 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) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain 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_properties_enums() (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.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory 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.RenameAtom 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.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge 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) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) deletes_property_enum() (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.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory 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.RenameAtom 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.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge 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) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain 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.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory 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.RenameAtom 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.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge 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) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) deletes_variant_enum() (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.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory 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.RenameAtom 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.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge 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) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) deletes_variants() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) deletes_variants_by_enum() (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) delRSteps_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) delRsteps_ (pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) delta (pyrosetta.rosetta.basic.sampling.orientations.QuatDBMetadata property) DELTA (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) delta (pyrosetta.rosetta.core.scoring.TorsionParams property) delta() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.SpringParams method) (pyrosetta.rosetta.protocols.dna.DNABase method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) delta2max (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) delta2min (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) delta3max (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) delta3min (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) DELTA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) delta_atr_score() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker.ProteinAtrRepChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) delta_chi_zz() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) delta_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) delta_cutoff (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) delta_cutoff() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) delta_cutoff_ (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric property) delta_filter_thresholds() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) delta_filters() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) delta_lengths() (pyrosetta.rosetta.protocols.splice.Splice method) delta_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) delta_omega1_range() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) delta_rep_score() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker.ProteinAtrRepChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) delta_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) delta_unsat_hbonds (pyrosetta.rosetta.protocols.analysis.InterfaceData property) delta_X_xx() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) delta_X_yy() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) delta_X_zz() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) deltaE_best() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) DeltaFilter (class in pyrosetta.rosetta.protocols.simple_filters) DeltaFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) deltaG_bind() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) deltaG_folding() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary method) denom() (in module pyrosetta.rosetta.protocols.cryst) DeNovoArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) DeNovoArchitectCreator (class in pyrosetta.rosetta.protocols.denovo_design.architects) DeNovoArchitectFactory (class in pyrosetta.rosetta.protocols.denovo_design.architects) DeNovoSilentFilePoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) DeNovoSilentFilePoseOutputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) dens_clear() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) dens_grad() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) dens_has_data() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) dens_pop() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) dens_push() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) dens_size() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) DenseBoolMap_5_0_t (class in pyrosetta.rosetta.utility) DenseEnergyContainer (class in pyrosetta.rosetta.core.scoring) DenseIGRepacker (class in pyrosetta.rosetta.protocols.pack_daemon) DenseNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) DenseNeighborIterator (class in pyrosetta.rosetta.core.scoring) DensePDEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) DensePDInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) DensePDNode (class in pyrosetta.rosetta.core.pack.interaction_graph) density (pyrosetta.rosetta.core.scoring.sc.Atom property) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData property) density() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) density_nbr() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) density_redraw (pyrosetta.rosetta.protocols.viewer.GraphicsState property) density_score() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) density_sigma (pyrosetta.rosetta.protocols.viewer.GraphicsState property) DensityFitResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) DensityFitResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) DensityGridSearchOptions (class in pyrosetta.rosetta.protocols.electron_density) DensityScoringClaimer (class in pyrosetta.rosetta.protocols.topology_broker) DensitySymmInfo (class in pyrosetta.rosetta.protocols.electron_density) DensityZscores (class in pyrosetta.rosetta.protocols.electron_density) DensityZscoresCreator (class in pyrosetta.rosetta.protocols.electron_density) DensityZscoresStatsSetup (class in pyrosetta.rosetta.core.scoring) DensSkeleton (class in pyrosetta.rosetta.protocols.loop_grower) DensStructInfo (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) DensStructInfoComp (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) dentropy_dbb() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) DenyPdbIdFilter (class in pyrosetta.rosetta.protocols.frag_picker) DEOXY_O2PRIME (pyrosetta.rosetta.core.chemical.VariantType attribute) DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) depc_ms (pyrosetta.rosetta.core.scoring.ScoreType attribute) DEPC_MS_Energy (class in pyrosetta.rosetta.core.energy_methods) DEPC_MS_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) depc_ms_input() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) DEPC_MS_SASA_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) 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() (pyrosetta.rosetta.core.optimization.DOF_Node method) dependent_atoms() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) dependent_dofs() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo 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) dependent_torsions() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) depends_on_a_true_index() (pyrosetta.rosetta.core.chemical.AtomICoor 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) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) DEPROTONATED (pyrosetta.rosetta.core.chemical.VariantType attribute) depth (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData property) depth() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) depth_ (pyrosetta.rosetta.protocols.viewer.triangle property) depth_first_connected_component_counting() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) dereference() (pyrosetta.rosetta.core.fragment.ConstFrameIterator method) (pyrosetta.rosetta.core.fragment.FragID_Iterator method) (pyrosetta.rosetta.core.fragment.FrameIterator method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileData.iterator method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose.const_iterator method) (pyrosetta.rosetta.core.select.Enumerate1WithSelector method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_connection_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_loadable_driver_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_statement_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_pool_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash.const_iterator method) (pyrosetta.rosetta.utility.Enumerate1 method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter method) (pyrosetta.rosetta.utility.graph.LowMemEdgeListIter method) (pyrosetta.rosetta.utility.LexicographicalIterator method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_scoring_bin_transitions_BinTransitionCalculator_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_antibody_AntibodyInfo_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_AtomProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_ResidueProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_rotamers_RotamerLibrarySpecification_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_scoring_ScoreFunction_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_BicubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_PolycubicSplineBase_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_MathNTensorBase_double_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_protocols_loops_Loops_t method) deriv() (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs method) (pyrosetta.rosetta.core.scoring.SpringParams method) deriv_atom_pair() (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) deriv_check() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.optimization.MinimizerOptions method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) deriv_check_result() (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.NumericalDerivCheckResult method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) deriv_check_to_stdout() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) deriv_check_verbose() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) deriv_cutoff_ (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) deriv_multiply() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) deriv_score() (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) deriv_type_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) derivative_atom() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) derivative_graph() (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) DerivativeFinder (class in pyrosetta.rosetta.core.scoring.lkball) DerivativeFinderWadj (class in pyrosetta.rosetta.core.scoring.lkball) derivatives() (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) DerivCheckDataPoint (class in pyrosetta.rosetta.core.optimization) 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) derived_process_deallocation_message() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) DerivedPeptideEntry (class in pyrosetta.rosetta.protocols.peptide_deriver) DerivedSequenceMapping (class in pyrosetta.rosetta.core.sequence) derivs() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) DerivVectorPair (class in pyrosetta.rosetta.core.scoring) DescentDirectionAlgorithm (class in pyrosetta.rosetta.core.optimization) describe() (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) 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.tag.XMLSchemaSimpleSubelementList.ElementSummary property) 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) deserialize() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.PartialAtomID method) (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (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.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) deserialize_data() (pyrosetta.rosetta.basic.mpi.DbMoverMessageListener method) deserialize_db_listener_data() (in module pyrosetta.rosetta.protocols.features) deserialize_xyz_coords() (in module pyrosetta.rosetta.protocols.features) DESIGN (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation attribute) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerOperationType attribute) design() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover 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.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect 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.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) design_all_aas() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) design_anchor_index() (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo 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_chain() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) design_chain1() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) design_chain2() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) design_chain_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) design_framework() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) design_layer() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) design_loop() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) design_matrix (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) design_mode (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) design_mover() (pyrosetta.rosetta.protocols.recon_design.MSDMover method) design_neighbor (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) design_neighbors() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) design_only_target_residues() (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) design_peptide (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) design_proline() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) design_protocol_enum_to_string() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) design_protocol_is_present() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) design_protocol_string_to_enum() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager 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) design_shell() (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) design_size() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) design_strategy() (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) design_supercharge() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) design_supercharge_AvNAPSA() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) design_targets() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) design_targets_score() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) design_task_factory() (pyrosetta.rosetta.protocols.splice.Splice method) design_type (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) designable (pyrosetta.rosetta.protocols.dna.PositionType property) DESIGNABLE (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation attribute) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerSpecificationType attribute) designable() (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) designable_only() (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) designable_residues() (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) DesignableResiduesFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) DesignableResiduesFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) DesignAroundApply() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) DesignAroundOperation (class in pyrosetta.rosetta.protocols.task_operations) DesignAroundOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) DesignContrast (class in pyrosetta.rosetta.core.io.sequence_comparation) designed_residue() (pyrosetta.rosetta.protocols.dna.PDBOutput method) designing_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) designing_with_noncanonicals() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) DesignInterfacesOperation (class in pyrosetta.rosetta.protocols.splice) DesignInterfacesOperationCreator (class in pyrosetta.rosetta.protocols.splice) DesignMeanField (class in pyrosetta.rosetta.protocols.mean_field) DesignMinimizeHbonds (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DesignMinimizeHbondsCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DesignProteinBackboneAroundDNA (class in pyrosetta.rosetta.protocols.dna) DesignProteinBackboneAroundDNACreator (class in pyrosetta.rosetta.protocols.dna) DesignProtocolEnum_total (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum attribute) DesignRepackMover (class in pyrosetta.rosetta.protocols.calc_taskop_movers) DesignRestrictions (class in pyrosetta.rosetta.core.pack.task.operation) DesignRestrictionsCreator (class in pyrosetta.rosetta.core.pack.task.operation) 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_charge() (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) desired_entity_history_size() (pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet 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_BASENAME method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS 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_ATOM method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE method) destination_size() (pyrosetta.rosetta.utility.subset_mapping method) destination_xyz (pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtom property) destroy() (pyrosetta.rosetta.RDKit.RDValue method) destroyRandomDecoys() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering 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.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t 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) det() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) det3() (in module pyrosetta.rosetta.numeric.model_quality) detach() (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.network.UIObserver 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.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.PDBInfo 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) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.network.UIObserver method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) (pyrosetta.rosetta.protocols.viewer.SilentObserver method) detach_from_conformation() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet 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) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet 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) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) detailed_balance() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) detailed_search() (pyrosetta.rosetta.protocols.hybridization.TMalign method) detailedControlsTagSetting (class in pyrosetta.rosetta.protocols.hybridization) detect() (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Json_based_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.core.pose.rna) 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.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) detect_connecting_subunits() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) detect_disulfides() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) detect_heavy_chain() (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector method) (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.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) detect_phosphate_contacts() (in module pyrosetta.rosetta.core.pose.rna) 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.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) detect_sugar_contacts() (in module pyrosetta.rosetta.core.pose.rna) DetectProteinLigandInterface (class in pyrosetta.rosetta.protocols.enzdes) DetectProteinLigandInterfaceOperationCreator (class in pyrosetta.rosetta.protocols.enzdes) DetectSymmetry (class in pyrosetta.rosetta.protocols.symmetry) DetectSymmetryMoverCreator (class in pyrosetta.rosetta.protocols.symmetry) determine_atom_inds_for_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) determine_atom_level_edge_info() (in module pyrosetta.rosetta.core.pack.hbonds) determine_atom_level_edge_info_for_all_edges() (in module pyrosetta.rosetta.core.pack.hbonds) determine_atom_level_node_info() (in module pyrosetta.rosetta.core.pack.hbonds) determine_atom_level_node_info_for_all_nodes() (in module pyrosetta.rosetta.core.pack.hbonds) 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_dna_interface() (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) determine_file_type() (in module pyrosetta.rosetta.core.import_pose) determine_flexible_regions() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) determine_heading_direction_by_vector() (in module pyrosetta.rosetta.protocols.features.strand_assembly) determine_interface() (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) determine_job_list() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) determine_job_list_and_track() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) determine_job_tag() (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) determine_largest_nbr_atom_distance() (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp static method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO static method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO static method) determine_lo_and_hi_residues() (in module pyrosetta.rosetta.core.scoring.methods) determine_loop() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) determine_max_accepted_hbond_count() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup static method) determine_num_for_partition() (in module pyrosetta.rosetta.protocols.jd3.dag_node_managers) determine_overlap() (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) determine_polarization_groups() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) determine_preliminary_job_list_from_xml_file() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) determine_protein_interface() (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) determine_ramachandran_hash() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) determine_ramachandran_hash_for_residue_with_dihedrals() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) determine_random_number_seed() (in module pyrosetta.rosetta.basic.random) determine_redundant_conformer_groups() (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) determine_redundant_upstream_matchres() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.OutputWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) determine_repeating_unit_offset() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) determine_res_cb_deviation() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) determine_residue_connection() (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFactory static method) determine_score_variations() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) determine_validity_of_stage_tags() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) determine_whether_point_is_buried() (in module pyrosetta.rosetta.core.select.util) deterministic_graft (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum attribute) dEtot_dEhb() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) dev (pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy property) deviation() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) dexponential() (in module pyrosetta.rosetta.core.scoring.constraints) dF() (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) dFdall() (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_1_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_2_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_3_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_4_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_5_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_6_t method) dFdx() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) dFdxi() (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_1_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_2_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_3_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_4_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_5_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_6_t method) dFdy() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) dFdz() (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) DFIRE (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) (pyrosetta.rosetta.core.scoring.ScoreType attribute) DFIRE_Energy (class in pyrosetta.rosetta.core.energy_methods.dfire) DFIRE_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods.dfire) DFIRE_Potential (class in pyrosetta.rosetta.core.scoring.methods.dfire) dfour1_plan() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) DFPMinConvergedAbsolute (class in pyrosetta.rosetta.core.optimization) DFPMinConvergedFractional (class in pyrosetta.rosetta.core.optimization) DFr (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) DFr_BAB (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) DFr_HPN (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) 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) dfs_cycle_finder() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) DFUNC (pyrosetta.rosetta.basic.ProfTag attribute) dfunc() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.func_1d method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMultifunc method) (pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc method) (pyrosetta.rosetta.core.scoring.CenHBPotential method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CB_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CBSG_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.SG_Dist_Func method) (pyrosetta.rosetta.core.scoring.disulfides.SGSG_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.CircularSplineFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.CountViolFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FadeFunc method) (pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.HarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.IdentityFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) (pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc method) (pyrosetta.rosetta.core.scoring.func.SigmoidFunc method) (pyrosetta.rosetta.core.scoring.func.SkipViolFunc method) (pyrosetta.rosetta.core.scoring.func.SmoothStepFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SplineFunc method) (pyrosetta.rosetta.core.scoring.func.SquareWell2Func method) (pyrosetta.rosetta.core.scoring.func.SquareWellFunc method) (pyrosetta.rosetta.core.scoring.func.SumFunc method) (pyrosetta.rosetta.core.scoring.func.TopOutFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs 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.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer 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.qsar.qsarOptFunc method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.TensorsOptimizer_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.TensorsOptimizer_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.TensorsOptimizer_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.TensorsOptimizer_Ts4 method) dfunc_component() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) dfunc_exact() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd method) dfunc_numeric() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd method) dfunc_soft() (pyrosetta.rosetta.core.scoring.CenHBPotential method) dG (pyrosetta.rosetta.protocols.analysis.InterfaceData property) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) dG_binding_correlation (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) dG_dCi() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) dG_dCi_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) dG_dSASA_ratio (pyrosetta.rosetta.protocols.analysis.InterfaceData property) dG_ins (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.tm_region property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.tm_region property) dG_ins_for_window() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) dG_term_for_residue_at_position() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) dgaussian() (in module pyrosetta.rosetta.core.scoring.constraints) DGBindOptEData (class in pyrosetta.rosetta.protocols.optimize_weights) dGfreeB() (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) dGfreeW() (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) dH (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) dH_pop() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) DHR_Type (class in pyrosetta.rosetta.protocols.docking) dhSASA (pyrosetta.rosetta.protocols.analysis.InterfaceData property) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) dhSASA_rel_by_charge (pyrosetta.rosetta.protocols.analysis.InterfaceData property) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) dhSASA_sc (pyrosetta.rosetta.protocols.analysis.InterfaceData property) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) Di() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) Di_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) diag() (pyrosetta.rosetta.numeric.xyzMatrix_double_t static method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t static method) DiagnosticData (class in pyrosetta.rosetta.basic.datacache) diagonal (pyrosetta.rosetta.core.sequence.AlignMove attribute) diagonalize_tensor() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) DIAMAGNETIC (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) Dict (class in pyrosetta.rosetta.RDKit) Dict.Pair (class in pyrosetta.rosetta.RDKit) DID_NOT_ADD_STRUCTURE (pyrosetta.rosetta.protocols.optimize_weights.AddStatus attribute) die() (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) die_for_unaccessed_options() (pyrosetta.rosetta.utility.tag.Tag method) die_for_unaccessed_options_recursively() (pyrosetta.rosetta.utility.tag.Tag method) diff_torsions (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) DiffAtomSasaFilter (class in pyrosetta.rosetta.protocols.enzdes) DiffAtomSasaFilterCreator (class in pyrosetta.rosetta.protocols.enzdes) difference_from() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) different_resgroup() (in module pyrosetta.rosetta.core.pack.rotamer_set) different_restype() (in module pyrosetta.rosetta.core.pack.rotamer_set) differentiate() (pyrosetta.rosetta.numeric.expression_parser.AbsoluteValueExpression method) (pyrosetta.rosetta.numeric.expression_parser.AddExpression method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.BinaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.DivideExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.ITEExpression method) (pyrosetta.rosetta.numeric.expression_parser.LiteralExpression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.expression_parser.MinExpression method) (pyrosetta.rosetta.numeric.expression_parser.MultiplyExpression method) (pyrosetta.rosetta.numeric.expression_parser.NaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.NotExpression method) (pyrosetta.rosetta.numeric.expression_parser.OrExpression method) (pyrosetta.rosetta.numeric.expression_parser.SquarerootExpression method) (pyrosetta.rosetta.numeric.expression_parser.SubtractExpression method) (pyrosetta.rosetta.numeric.expression_parser.UnaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.VariableExpression method) (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.ExpExpression method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.LnExpression method) (pyrosetta.rosetta.protocols.pack_daemon.Mean method) (pyrosetta.rosetta.protocols.pack_daemon.PowExpression method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2 method) (pyrosetta.rosetta.protocols.pack_daemon.VMax method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMin method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) diffuse_ring() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid 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) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector 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_const() (pyrosetta.rosetta.protocols.splice.Splice method) dihedral_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) dihedral_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge 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) dihedral_weight() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) dihedralA (pyrosetta.rosetta.protocols.jumping.cstType attribute) dihedralAB (pyrosetta.rosetta.protocols.jumping.cstType attribute) dihedralB (pyrosetta.rosetta.protocols.jumping.cstType attribute) DihedralConstraint (class in pyrosetta.rosetta.core.scoring.constraints) DihedralConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) DihedralConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) DihedralConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) DihedralConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores)

DihedralDistanceMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) DihedralDistanceMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) DihedralPairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) DihedralPairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) dihedrals() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom method) dihedrals_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) DIIODINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) dijkstras() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) dim() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) dim_labels() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) Dimension (class in pyrosetta.rosetta.ObjexxFCL) dimension() (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.RDGeom.Point method) (pyrosetta.rosetta.RDGeom.Point3D method) dimensionality() (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_1_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_2_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_3_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_4_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_5_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_6_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSplineBase method) (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_bool_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_double_t method) 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) dimensions() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) dimensions_initialized() (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) dimer_neighbor (pyrosetta.rosetta.core.scoring.Strands property) DimerPairing (class in pyrosetta.rosetta.protocols.fldsgn.topology) DimerPairings (class in pyrosetta.rosetta.protocols.fldsgn.topology) DIMETHYLATED_CTERMINUS (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) DIMETHYLATED_CTERMINUS_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) DIMETHYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) 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) dimsize() (pyrosetta.rosetta.utility.LexicographicalIterator method) dimsizes() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.protocols.match.Bool3DGrid method) DipolarCoupling (class in pyrosetta.rosetta.core.scoring) DipolarCouplingEnergy (class in pyrosetta.rosetta.core.energy_methods) DipolarCouplingEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleParameter method) dir() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) DirectedEdge (class in pyrosetta.rosetta.utility.graph) 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) DirectedNode (class in pyrosetta.rosetta.utility.graph) Direction (class in pyrosetta.rosetta.protocols.rigid) direction (pyrosetta.rosetta.protocols.hotspot_hashing.VectorPair property) direction() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) directionVector() (pyrosetta.rosetta.RDGeom.Point3D method) directory() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) DirectReadoutEnergy (class in pyrosetta.rosetta.core.energy_methods) DirectReadoutEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DirectReadoutPotential (class in pyrosetta.rosetta.core.scoring.dna) DirectSegmentLookup (class in pyrosetta.rosetta.protocols.indexed_structure_store) DirectSegmentLookupConfig (class in pyrosetta.rosetta.protocols.indexed_structure_store) DirectSegmentLookupMover (class in pyrosetta.rosetta.protocols.indexed_structure_store.movers) DirectSegmentLookupMoverCreator (class in pyrosetta.rosetta.protocols.indexed_structure_store.movers) DirectSegmentLookupResult (class in pyrosetta.rosetta.protocols.indexed_structure_store) DirStructureStoreBackend (class in pyrosetta.rosetta.protocols.indexed_structure_store) dis() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) dis_U1D1 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleConstraint property) dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) disAB (pyrosetta.rosetta.protocols.jumping.cstType attribute) disable() (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) disable_AAs() (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities 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_fitness_evaluation() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover 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_metapatches() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder 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_restypes() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) disable_restypes_with_at_least_one_property() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) disable_sampling_of_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) disable_total_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) DisableAntibodyRegionOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) DisableAntibodyRegionOperationCreator (class in pyrosetta.rosetta.protocols.antibody.task_operations) DisableCDRsOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) DisableCDRsOperationCreator (class in pyrosetta.rosetta.protocols.antibody.task_operations) disabled_except_during_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) disallow_aa() (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) disallow_aas() (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) disallow_bps_at_extra_min_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) disallow_current_slide() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) disallow_movement_of_input_res() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) disallow_pack_polar_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) disallow_properties() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) disallow_quench() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) disallow_realign() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) disallow_resid() (pyrosetta.rosetta.core.pack.task.operation.OptH method) disallow_variants() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) DisallowIfNonnative (class in pyrosetta.rosetta.core.pack.task.operation) DisallowIfNonnativeCreator (class in pyrosetta.rosetta.core.pack.task.operation) DisallowIfNonnativeRLT (class in pyrosetta.rosetta.core.pack.task.operation) DisallowIfNonnativeRLTCreator (class in pyrosetta.rosetta.core.pack.task.operation) discard() (pyrosetta.bindings.pose.ResidueLabelAccessor method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet method) (pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t method) (pyrosetta.rosetta.std.set_core_id_DOF_ID_t method) (pyrosetta.rosetta.std.set_core_id_PartialAtomID_t method) (pyrosetta.rosetta.std.set_double_t method) (pyrosetta.rosetta.std.set_int_t method) (pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.set_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t method) (pyrosetta.rosetta.std.set_std_string_t method) (pyrosetta.rosetta.std.set_unsigned_long_t method) discard_conformation_domain_map() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) discard_job_result() (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) discard_old_entity (pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage attribute) DISCONNECT (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent attribute) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag attribute) disconnect_segments() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) disconnected_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) discontinued_lower() (in module pyrosetta.rosetta.protocols.hybridization) discontinued_upper() (in module pyrosetta.rosetta.protocols.hybridization) discouraged_properties() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) DiscreteIntervalEncodingTree_unsigned_long_t (class in pyrosetta.rosetta.numeric) DiscreteRandomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) DisembodiedAssembly (class in pyrosetta.rosetta.protocols.legacy_sewing) disjoint_set_sizes() (pyrosetta.rosetta.utility.graph.DisjointSets method) DisjointSets (class in pyrosetta.rosetta.utility.graph) display() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) display_constraint_residues() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) display_secstruct() (in module pyrosetta.bindings.pose) (pyrosetta.rosetta.core.pose.Pose method) DisplayPoseLabelsMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) DisplayPoseLabelsMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) dispose() (pyrosetta.rosetta.cppdb.backend.connection static method) (pyrosetta.rosetta.cppdb.backend.driver static method) (pyrosetta.rosetta.cppdb.backend.loadable_driver static method) (pyrosetta.rosetta.cppdb.backend.result static method) (pyrosetta.rosetta.cppdb.backend.statement static method) (pyrosetta.rosetta.cppdb.pool static method) (pyrosetta.rosetta.cppdb.ref_counted static method) dist (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment property) (pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList property) dist() (pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint 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.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.cluster.calibur.Stru method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) (pyrosetta.rosetta.protocols.frag_picker.Contact method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) (pyrosetta.rosetta.protocols.hybridization.TMalign method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) dist2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) dist2_cut() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) dist_cutoff() (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) dist_exponent() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) dist_map() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) dist_midpoint() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) dist_square() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) dist_squared() (pyrosetta.rosetta.protocols.frag_picker.Contact method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker method) dist_track() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord method) distance (pyrosetta.rosetta.core.scoring.atomic_depth.volumepixel property) DISTANCE (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel attribute) (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel.CONFORMER_FILTER attribute) distance (pyrosetta.rosetta.core.scoring.sc._RESULTS property) (pyrosetta.rosetta.protocols.antibody.CDRDBPose property) (pyrosetta.rosetta.protocols.antibody.CDRDBSequence property) 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.orbitals.ICoorOrbitalData method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType 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.core.scoring.saxs.DistanceHistogram method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.ClusteringTreeNode method) (pyrosetta.rosetta.numeric.kdtree.KDNode method) (pyrosetta.rosetta.numeric.kdtree.KDPoint method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetric method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) distance_ (pyrosetta.rosetta.protocols.legacy_sewing.Model property) distance_bound() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) distance_chainbreak (pyrosetta.rosetta.core.scoring.ScoreType attribute) distance_cutoff() (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) distance_diff() (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) distance_fast() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) distance_from_line2D() (in module pyrosetta.rosetta.core.membrane) distance_internal() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) distance_matrix() (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) distance_pair() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) distance_potential_histogram() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) distance_record() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) distance_slow() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) distance_squared (pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy property) distance_squared() (in module pyrosetta.rosetta.core.kinematics.tree) (pyrosetta.rosetta.core.kinematics.RT method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t 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) distance_threshold() (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) distance_weight() (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) DistanceChainbreakEnergy (class in pyrosetta.rosetta.core.energy_methods) DistanceChainbreakEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DistanceConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) DistanceConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) distanceFromStart (pyrosetta.rosetta.protocols.toolbox.Node property) DistanceFunc (class in pyrosetta.rosetta.core.scoring.custom_pair_distance) DistanceHistogram (class in pyrosetta.rosetta.core.scoring.saxs) 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.energy_methods.GoapEnergy method) disth (pyrosetta.rosetta.protocols.kinmatch.KRSQuery property) distinguish_backbone_and_sidechain() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) distinguish_backbone_and_sidechain_for_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) distinguish_pucker() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) Distribution (class in pyrosetta.rosetta.protocols.ligand_docking) distribution (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info property) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info property) DistributionMap (class in pyrosetta.rosetta.protocols.ligand_docking) disulf_atom_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) DISULFIDE (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) disulfide() (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) disulfide_atom_indices() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) DISULFIDE_BONDED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) disulfide_bonded() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) disulfide_bonds() (in module pyrosetta.rosetta.core.conformation) disulfide_cutpoint (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) disulfide_jump_points (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) disulfide_label() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) disulfide_list() (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover static method) disulfide_matching_energy (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) disulfide_pairs() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) disulfide_pairs_from_sfr() (in module pyrosetta.rosetta.core.pose) disulfide_positions_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) disulfide_ss (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) DisulfideAtomIndices (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideCyclizationViability (class in pyrosetta.rosetta.protocols.simple_moves) DisulfideDerivativeAtom (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) DisulfideEntropyFilter (class in pyrosetta.rosetta.protocols.simple_filters) DisulfideEntropyFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) DisulfideFile (class in pyrosetta.rosetta.core.io.raw_data) DisulfideFile.NumberingSystem (class in pyrosetta.rosetta.core.io.raw_data) DisulfideFile.ResNum (class in pyrosetta.rosetta.core.io.raw_data) DisulfideFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) DisulfideFilterCreator (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) DisulfideInsertionMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) DisulfideMatchingDatabase (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingEnergy (class in pyrosetta.rosetta.core.energy_methods) DisulfideMatchingEnergyComponents (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingEnergyContainer (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DisulfideMatchingNeighborConstIterator (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingNeighborIterator (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMatchingPotential (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfideMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DisulfideMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DisulfideOptimizationMover (class in pyrosetta.rosetta.protocols.minimization_packing) DisulfideOptimizationMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) disulfides() (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) disulfides_bb() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) disulfides_side() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) DisulfidizeMover (class in pyrosetta.rosetta.protocols.denovo_design) DisulfidizeMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design) DisulfJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) disulfLandingRange (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) disulfMobileRange (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) DisulfPairing (class in pyrosetta.rosetta.protocols.jumping) DisulfPairingLibrary (class in pyrosetta.rosetta.protocols.jumping) DisulfResNeighbConstIterator (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfResNeighbIterator (class in pyrosetta.rosetta.core.scoring.disulfides) DisulfTemplate (class in pyrosetta.rosetta.protocols.jumping) diversify() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) diversify_all_confs() (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) diversify_backbone_only_rotamers() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) diversify_cst_conformers() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) diversify_dof_conformers() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump 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) diversityfilter() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) divide_and_conquer() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) DIVIDE_SYMBOL (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) DivideAndConqueror (class in pyrosetta.rosetta.protocols.denovo_design.components) DivideExpression (class in pyrosetta.rosetta.numeric.expression_parser) divides_backbone_and_sidechain_energetics() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) dk() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) dK_dphi() (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters method) dK_dpsi() (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters method) DL (pyrosetta.rosetta.core.chemical.carbohydrates.RootData property) 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) dlk_frac_sigmoid() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) dm() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) DME_FilterMover (class in pyrosetta.rosetta.protocols.simple_moves) DMS (pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType attribute) DMS_values() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) dmu_dphi() (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters method) dmu_dpsi() (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters method) dmy_lk_fraction() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) DNA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) dna_base_distance (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_base_partner() (in module pyrosetta.rosetta.protocols.dna) DNA_BaseEnergy (class in pyrosetta.rosetta.core.energy_methods) DNA_BaseEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DNA_BasePotential (class in pyrosetta.rosetta.core.scoring.dna) dna_bb_torsion (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_bp (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_bs (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_chains() (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) dna_chi (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_comp_name_str() (in module pyrosetta.rosetta.protocols.dna) dna_dihedral_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_dihedral_chi (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_dihedral_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) dna_dihedral_sugar (pyrosetta.rosetta.core.scoring.ScoreType attribute) DNA_DihedralEnergy (class in pyrosetta.rosetta.core.energy_methods) DNA_DihedralEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DNA_DihedralPotential (class in pyrosetta.rosetta.core.scoring.dna) dna_dr (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_env (pyrosetta.rosetta.core.scoring.ScoreType attribute) DNA_EnvPairEnergy (class in pyrosetta.rosetta.core.energy_methods) DNA_EnvPairEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DNA_EnvPairPotential (class in pyrosetta.rosetta.core.scoring.dna) dna_full_name3() (in module pyrosetta.rosetta.protocols.dna) dna_neighbors() (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) dna_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) dna_positions() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) dna_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) DNA_ReferenceEnergy (class in pyrosetta.rosetta.core.energy_methods) DNA_ReferenceEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) dna_seq_tag() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) dna_sugar_close (pyrosetta.rosetta.core.scoring.ScoreType attribute) DNABase (class in pyrosetta.rosetta.protocols.dna) DNABasepair (class in pyrosetta.rosetta.protocols.dna) DNABasestep (class in pyrosetta.rosetta.protocols.dna) DNABFormPotential (class in pyrosetta.rosetta.core.scoring.dna) DnaChains (class in pyrosetta.rosetta.protocols.dna) DNAChiEnergy (class in pyrosetta.rosetta.core.energy_methods) DNAChiEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DNAClashCheckFilter (class in pyrosetta.rosetta.protocols.dna_dock) DNAClashCheckFilterCreator (class in pyrosetta.rosetta.protocols.dna_dock) DnaDesignDef (class in pyrosetta.rosetta.protocols.dna) DnaInterfaceFinder (class in pyrosetta.rosetta.protocols.dna) DnaInterfaceMinMover (class in pyrosetta.rosetta.protocols.dna) DnaInterfaceMinMoverCreator (class in pyrosetta.rosetta.protocols.dna) DnaInterfaceMultiStateDesign (class in pyrosetta.rosetta.protocols.dna) DnaInterfaceMultiStateDesignCreator (class in pyrosetta.rosetta.protocols.dna) DnaInterfacePacker (class in pyrosetta.rosetta.protocols.dna) DnaInterfacePackerCreator (class in pyrosetta.rosetta.protocols.dna) DNAMethyltransferaseMover (class in pyrosetta.rosetta.protocols.enzymatic_movers) DNAMethyltransferaseMoverCreator (class in pyrosetta.rosetta.protocols.enzymatic_movers) DnaNeighbor (class in pyrosetta.rosetta.protocols.dna) DNAParameters (class in pyrosetta.rosetta.protocols.dna) DnaPosition (class in pyrosetta.rosetta.protocols.dna) DNATorsionEnergy (class in pyrosetta.rosetta.core.energy_methods) DNATorsionEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) DNATorsionPotential (class in pyrosetta.rosetta.core.scoring.dna) dncase() (in module pyrosetta.rosetta.ObjexxFCL) dneglnrotprob_dbb() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dnmtr() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) dnmtr_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) do_apply() (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) do_caching() (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (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.CachingScoringMethod 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.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance 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.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore 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_calibration() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) do_clustering() (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle 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_fullatom_refinement() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) do_I_skip() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) do_init() (pyrosetta.rosetta.protocols.rpc.BasicCmdLineInit method) (pyrosetta.rosetta.protocols.rpc.BasicInit method) do_intrastage_docking() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) do_matching() (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) do_minimization() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) do_not_autoassign_SS() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) do_not_sample_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) do_one_line() (in module pyrosetta.rosetta.protocols.frag_picker.scores) do_optimized_transform() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) do_packing() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) do_prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) do_random_moves() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) do_redistribution() (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) do_rerun() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) do_rotation() (pyrosetta.rosetta.protocols.hybridization.TMalign method) do_score() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) do_scoring() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) do_screen() (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) do_set_xyz() (in module pyrosetta.rosetta.protocols.stepwise.sampler.protein) do_stage1_conformation_initialization() (in module pyrosetta.rosetta.protocols.glycan_docking) do_stage1_tor_uniform_perturbation() (in module pyrosetta.rosetta.protocols.glycan_docking) do_stage2_sample_pack_min_cycle() (in module pyrosetta.rosetta.protocols.glycan_docking) do_test_move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) do_the_modeler() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) do_the_move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) do_xy_scan() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) dock_chunks() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) dock_chunks_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) DOCK_DOMAIN (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) dock_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) dock_each_chunk() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) dock_each_chunk_per_chain() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) dock_ens_conf (pyrosetta.rosetta.core.scoring.ScoreType attribute) dock_high_res() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) dock_into_density() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) dock_into_density_legacy() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) dock_low_res() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) DockAndRetrieveSidechains (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DockAndRetrieveSidechainsCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DockFragmentsIntoDensityMover (class in pyrosetta.rosetta.protocols.electron_density) docking() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) docking_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) docking_highres_filter() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) docking_highres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) docking_jump() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) docking_lowres_filter() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) docking_lowres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) docking_move_size() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) DockingEnsemble (class in pyrosetta.rosetta.protocols.docking) DockingEnsemblePrepackProtocol (class in pyrosetta.rosetta.protocols.docking) DockingHighRes (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) (pyrosetta.rosetta.protocols.docking.DHR_Type attribute) DockingHighResLegacyCreator (class in pyrosetta.rosetta.protocols.docking) DockingInitialPerturbation (class in pyrosetta.rosetta.protocols.docking) DockingInitialPerturbationCreator (class in pyrosetta.rosetta.protocols.docking) DockingLowRes (class in pyrosetta.rosetta.protocols.docking) DockingLowResEnsemble (class in pyrosetta.rosetta.protocols.docking) DockingLowResFilter (class in pyrosetta.rosetta.protocols.docking) DockingNoRepack1 (class in pyrosetta.rosetta.protocols.simple_task_operations) DockingNoRepack2 (class in pyrosetta.rosetta.protocols.simple_task_operations) DockingPrepackProtocol (class in pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.docking.DHR_Type attribute) DockingPrepackProtocolCreator (class in pyrosetta.rosetta.protocols.docking) DockingProtocol (class in pyrosetta.rosetta.protocols.docking) DockingProtocolCreator (class in pyrosetta.rosetta.protocols.docking) DockingScoreFunction (class in pyrosetta.rosetta.core.scoring) DockingSlideIntoContact (class in pyrosetta.rosetta.protocols.docking) DockingSlideIntoContactCreator (class in pyrosetta.rosetta.protocols.docking) DockLatticeMover (class in pyrosetta.rosetta.protocols.cryst) DockLatticeMoverCreator (class in pyrosetta.rosetta.protocols.cryst) DockMCMCycle (class in pyrosetta.rosetta.protocols.docking) DockMCMProtocol (class in pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.docking.DHR_Type attribute) DockMCMProtocolCreator (class in pyrosetta.rosetta.protocols.docking) DockMinMover (class in pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.docking.DHR_Type attribute) DockMinMoverCreator (class in pyrosetta.rosetta.protocols.docking) DockPDBIntoDensityMover (class in pyrosetta.rosetta.protocols.electron_density) dockPoseIntoMap() (in module pyrosetta.rosetta.protocols.electron_density) DockSetupMover (class in pyrosetta.rosetta.protocols.docking) DockSetupMoverCreator (class in pyrosetta.rosetta.protocols.docking) DockTaskFactory (class in pyrosetta.rosetta.protocols.docking) DockWithHotspotMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) DockWithHotspotMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) doCleanups() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) does_final_fold_tree_exist() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) DOES_NOT_CONTROL (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength attribute) (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength.PrioSubtype attribute) (pyrosetta.rosetta.protocols.environment.claims.ControlStrength attribute) does_overlap() (pyrosetta.rosetta.core.scoring.packstat.Circle method) 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.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) dof_access() (pyrosetta.rosetta.core.environment.DofPassport 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_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) DOF_DataPoint (class in pyrosetta.rosetta.core.optimization) dof_derivative() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer 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.optimization.DOF_DataPoint method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) DOF_ID_Map_bool_t (class in pyrosetta.rosetta.core.id) DOF_ID_Map_core_id_TorsionID_t (class in pyrosetta.rosetta.core.id) DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t (class in pyrosetta.rosetta.core.id) DOF_ID_Range (class in pyrosetta.rosetta.core.id) dof_is_independent() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) DoF_name() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) DOF_Node (class in pyrosetta.rosetta.core.optimization) dof_node() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) dof_node_for_chi() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) dof_node_from_id() (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) dof_nodes() (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) dof_sample_index() (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) DoF_sample_value() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) dof_step_data() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) dof_type (class in pyrosetta.rosetta.core.conformation.symmetry) DOF_Type (class in pyrosetta.rosetta.core.id) DoF_type() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) DOF_type_is_rb() (in module pyrosetta.rosetta.core.id) dof_val() (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) DofClaim (class in pyrosetta.rosetta.protocols.topology_broker.claims) DofClaim.ClaimRight (class in pyrosetta.rosetta.protocols.topology_broker.claims) DOFElement (class in pyrosetta.rosetta.protocols.environment.claims) DOFHistogramRecorder (class in pyrosetta.rosetta.protocols.simple_moves) dofmover_compresses() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) DofPassport (class in pyrosetta.rosetta.core.environment) dofs() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) dofs_info() (pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo method) dofs_to_vars() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) dofType (class in pyrosetta.rosetta.protocols.jumping) DofUnlock (class in pyrosetta.rosetta.protocols.environment) doi() (pyrosetta.rosetta.basic.citation_manager.Citation method) domain_map() (pyrosetta.rosetta.core.kinematics.MinimizerMapBase method) (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) domain_parse_templates() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) DomainAssembly (class in pyrosetta.rosetta.protocols.abinitio) (class in pyrosetta.rosetta.protocols.hybridization) DomainAssemblyCreator (class in pyrosetta.rosetta.protocols.abinitio) DomainInterfaceFilter (class in pyrosetta.rosetta.protocols.simple_filters) doMD() (pyrosetta.rosetta.protocols.cartesian.MolecularDynamics method) dome_water_dist2() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) dominant() (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) (pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) doMinimising() (pyrosetta.rosetta.protocols.cartesian.MolecularDynamics method) don_atm_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) don_bbg_in_bb_bb_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) don_chem_type_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) don_deriv (pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs property) don_dist_cutoff() (pyrosetta.rosetta.protocols.features.WaterFeatures method) don_hatm() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) don_hatm_is_backbone() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) don_hatm_is_protein_backbone() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) don_index() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) don_npd_weight() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) don_occ_type_has_data() (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) don_occ_type_mapping() (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) don_res() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) don_res_is_dna() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) don_res_is_protein() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) don_rsd_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) don_strength() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) don_type() (pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple method) don_type_has_data() (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) don_type_mapping() (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) don_wt_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) don_wt_alt_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) done_submitting() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) donor() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) donor_acceptor_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) donor_acceptor_groups() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_accepted() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_acceptor_groups_equivalent_res_symmetry_copy_hbonds_donated() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_acceptor_groups_intrares_hbonds_accepted() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_acceptor_groups_intrares_hbonds_donated() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) donor_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) donor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) donor_symmetry_copy_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) donorList (pyrosetta.rosetta.protocols.sparta.PDB property) 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) dont_compute_cav_balls (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) dont_fail_if_no_solution_found() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) dont_mutate_correct_charge() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) dont_mutate_glyprocys() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) dont_mutate_hbonded_sidechains() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) dontype (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon property) 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) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) dot_abs() (pyrosetta.rosetta.core.scoring.EnergyEdge method) dot_coord() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots static method) dot_exposed() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) dot_product() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) dotProduct() (pyrosetta.rosetta.RDGeom.Point3D 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_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) double_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) DOUBLE_T_LOOP (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) DOUBLE_VESICLE (pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION attribute) DoubleBond (pyrosetta.rosetta.core.chemical.BondName attribute) DoubleBondOrder (pyrosetta.rosetta.core.chemical.BondOrder attribute) DoubleDenseIGRepacker (class in pyrosetta.rosetta.protocols.pack_daemon) DoubleDensePDEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) DoubleDensePDInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) DoubleDensePDNode (class in pyrosetta.rosetta.core.pack.interaction_graph) DoubleLayerKinematicAbinitio (class in pyrosetta.rosetta.protocols.abinitio) DoubleLazyEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) DoubleLazyInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) DoubleLazyNode (class in pyrosetta.rosetta.core.pack.interaction_graph) doubles_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) DoubleVesicle (class in pyrosetta.rosetta.core.conformation.membrane.membrane_geometry) DOWN (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) down_cast() (in module pyrosetta.rosetta.utility) DownJumpSRFD (class in pyrosetta.rosetta.core.fragment) download_from_web() (in module pyrosetta.toolbox.rcsb) download_model_if_not_existing() (pyrosetta.rosetta.protocols.esm_perplexity.EsmPerplexityTensorflowProtocol static method) downsample_pfront_poses() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) 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_atoms_required_inside_active_site() (pyrosetta.rosetta.protocols.match.MatcherTask 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.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) downstream_conf_id (pyrosetta.rosetta.protocols.match.match_dspos1 property) downstream_conf_id() (pyrosetta.rosetta.protocols.match.downstream_hit method) (pyrosetta.rosetta.protocols.match.Hit method) downstream_hit (class in pyrosetta.rosetta.protocols.match) 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) downstream_orientation_atoms() (pyrosetta.rosetta.protocols.match.MatcherTask method) downstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherTask method) downstream_pose_from_hit() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) downstream_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) downstream_res_nr() (pyrosetta.rosetta.protocols.jumping.JumpSample method) downstream_residues_from_jump() (in module pyrosetta.rosetta.protocols.hybridization) DownstreamAlgorithm (class in pyrosetta.rosetta.protocols.match.downstream) DownstreamBuilder (class in pyrosetta.rosetta.protocols.match.downstream) DownstreamCoordinateKinemageWriter (class in pyrosetta.rosetta.protocols.match.output) DownstreamRMSEvaluator (class in pyrosetta.rosetta.protocols.match.output) dp() (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) DP_iter() (pyrosetta.rosetta.protocols.hybridization.TMalign method) DP_Matrix (class in pyrosetta.rosetta.core.sequence) DPScoringScheme (class in pyrosetta.rosetta.core.sequence) dr_cycles() (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) draw_random_mainchain_torsion_values() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) draw_random_phi_psi_from_extra_cdf() (pyrosetta.rosetta.core.scoring.Ramachandran method) drawn_out_heavyatom_hydrogenatom_energy() (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) drdz (pyrosetta.rosetta.core.scoring.packstat.Circle property) drift() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) driver (class in pyrosetta.rosetta.cppdb.backend) (pyrosetta.rosetta.cppdb.connection_info property) driver() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) drop_aa_submatrix() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) drop_all_edges() (pyrosetta.rosetta.core.conformation.PointGraphPy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) drop_all_edges_for_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemGraphBase method) drop_all_submatrices() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) drop_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) drop_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Node method) drop_random_rate() (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) drop_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet 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.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) drop_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) drop_rotamers_by_index() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet 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.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) drop_small_submatrices_where_possible() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) drop_strand_pairs() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) drop_unfolded_pose() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) drop_unsatisfied_voxels() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) drop_zero_submatrices_where_possible() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) drotprob_dbb() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) dround() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) dry_run() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) Ds (pyrosetta.rosetta.core.chemical.element.Elements attribute) ds_find() (pyrosetta.rosetta.utility.graph.DisjointSets 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) ds_make_set() (pyrosetta.rosetta.utility.graph.DisjointSets method) DS_Node (class in pyrosetta.rosetta.utility.graph) ds_union() (pyrosetta.rosetta.utility.graph.DisjointSets method) dSA_dDi() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) dSA_dDi_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) dSASA (pyrosetta.rosetta.protocols.analysis.InterfaceData property) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) dSASA_fraction (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) dSASA_sc (pyrosetta.rosetta.protocols.analysis.InterfaceData property) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) dscore (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.mutt property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.mutt property) dscore() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMBondLengthScore method) dslf_ca_dih (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslf_ca_dih() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyComponents method) dslf_cbs_ds (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslf_cbs_ds() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyComponents method) dslf_cs_ang (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslf_cs_ang() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyComponents method) dslf_fa13 (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslf_fa13() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyComponents method) dslf_fa13_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslf_ss_dih (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslf_ss_dih() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyComponents method) dslf_ss_dst (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslf_ss_dst() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyComponents method) dslfc_ang (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslfc_ang() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_bb_dih (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslfc_bb_dih() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cb_dih (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslfc_cb_dih() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cb_dst (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslfc_cb_dst() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_cen_dst (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslfc_cen_dst() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents method) dslfc_rot (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslfc_rot() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) dslfc_RT (pyrosetta.rosetta.core.scoring.ScoreType attribute) dslfc_RT() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) dslfc_trans (pyrosetta.rosetta.core.scoring.ScoreType attribute) 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.facts.FACTSResidueInfo method) dsolv_dBR_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) dspos (pyrosetta.rosetta.protocols.match.match_dspos1 property) dspos1_mode() (pyrosetta.rosetta.protocols.match.output.BestMatchesCollection method) dsq() (pyrosetta.rosetta.core.conformation.AtomGraphEdgeData method) (pyrosetta.rosetta.core.conformation.PointGraphEdgeData method) dss_kappa1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_kappa2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_logA1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_logA2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_mixed_kappa1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_mixed_kappa2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_mixed_logA1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_mixed_logA2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_mixed_mu1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_mixed_mu2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_mu1 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) dss_mu2 (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) Dssp (class in pyrosetta.rosetta.core.scoring.dssp) dssp (pyrosetta.rosetta.protocols.features.SecondaryStructureSegment property) (pyrosetta.rosetta.protocols.features.Segment property) dssp() (in module pyrosetta.rosetta.protocols.simple_filters) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) dssp1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) dssp2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) dssp_ (pyrosetta.rosetta.protocols.legacy_sewing.SewSegment property) 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) dssp_updated_ss (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) DsspDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) DsspDesignOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) DsspMover (class in pyrosetta.rosetta.protocols.moves) DsspMoverCreator (class in pyrosetta.rosetta.protocols.moves) DsspShiftArray (class in pyrosetta.rosetta.protocols.pose_sewing.data_storage) DsspSpecificLengthRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) DsspSpecificLengthRequirementCreator (class in pyrosetta.rosetta.protocols.sewing.requirements) dst() (pyrosetta.rosetta.utility.SimulateMPIMessage method) dsurf (pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv property) dt() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) dtest_cutoff() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) DualMonteCarlo (class in pyrosetta.rosetta.protocols.moves) dualspace (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) dualspace() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) dummy_AlignmentAtomArrayInternalType() (in module pyrosetta.rosetta.core.kinematics.inverse) dummy_cacheable_data_type (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) dummy_InternalCoordAtoms() (in module pyrosetta.rosetta.core.kinematics.inverse) dummy_InternalCoordGeometry() (in module pyrosetta.rosetta.core.kinematics.inverse) dummy_modify() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) dummy_score_type (pyrosetta.rosetta.core.scoring.ScoreType attribute) DummyClass (class in pyrosetta.rosetta.protocols.toolbox) dump() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.func_1d method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMultifunc method) (pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc method) (pyrosetta.rosetta.protocols.checkpoint.FileBuffer 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.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer 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.qsar.qsarOptFunc method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.TensorsOptimizer_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.TensorsOptimizer_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.TensorsOptimizer_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.TensorsOptimizer_Ts4 method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) dump_aligned_motif() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) dump_as_pdb() (in module pyrosetta.rosetta.protocols.toolbox) dump_atom_pair_energy_table() (in module pyrosetta.toolbox.atom_pair_energy) dump_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_BRIX() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) dump_centroid() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) 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_conformer() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) dump_cst_file() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) dump_debug_pdb() (pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck method) dump_dome_bridge_waters_ (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy property) dump_dome_waters_ (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy property) dump_eggshell() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) dump_file() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) dump_frames_as_pdb() (in module pyrosetta.rosetta.core.fragment) dump_freq() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) dump_gws() (in module pyrosetta.rosetta.core.io.carbohydrates) dump_gws_chain() (in module pyrosetta.rosetta.core.io.carbohydrates) dump_initial_results() (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) 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_linkers() (pyrosetta.rosetta.protocols.sic_dock.LinkerScore method) dump_loophash_linkers() (in module pyrosetta.rosetta.protocols.sic_dock) dump_matching_motifs() (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) dump_minimal_pdb() (pyrosetta.rosetta.protocols.sic_dock.Rose method) dump_mmtf() (in module pyrosetta.rosetta.core.io.mmtf) (pyrosetta.rosetta.core.pose.Pose method) dump_motif() (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyCalciumMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyInterModelMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyPartnerMotifScorer method) dump_motif_hit() (pyrosetta.rosetta.protocols.motifs.MotifHit method) dump_motifs_pdb() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) dump_multimodel_pdb() (in module pyrosetta.rosetta.core.io.pdb) dump_oriented_pose_and_fp_to_pdb() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) 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.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.sic_dock.Rose method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) dump_pdb_name() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) dump_pdb_residue() (in module pyrosetta.rosetta.core.io.pdb) dump_pdb_to_file() (pyrosetta.rosetta.protocols.helix_capper.HelixNCapperMover method) (pyrosetta.rosetta.protocols.vip.VIP_Mover method) dump_pdb_when_fail() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) dump_pdbs() (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) dump_points_pdb() (in module pyrosetta.rosetta.protocols.sic_dock) dump_points_to_search_to_pdb_or_txt() (in module pyrosetta.rosetta.protocols.electron_density) dump_pose() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer 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_fname() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) dump_pose_kinemage() (in module pyrosetta.rosetta.protocols.viewer) dump_poses() (pyrosetta.rosetta.protocols.md.CartesianMD method) dump_pymol() (pyrosetta.rosetta.protocols.jumping.JumpSample method) dump_reference_pose() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_resfile() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) dump_residue_pair_energies() (in module pyrosetta.toolbox.atom_pair_energy) dump_score_line() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) dump_scored_pdb() (pyrosetta.rosetta.core.pose.Pose method) dump_scoring_table() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) dump_side_chains() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) dump_silent() (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) dump_stems() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) dump_table() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) dump_templates() (in module pyrosetta.rosetta.protocols.tcr) dump_trajectory (pyrosetta.rosetta.core.scoring.ScoreType attribute) dump_trajectory_gz() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) dump_trajectory_prefix() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) dump_trajectory_stride() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) dump_transfac() (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) dump_trisbpy() (pyrosetta.rosetta.protocols.sic_dock.scores.TrisBpyScore method) dump_vall_fasta() (in module pyrosetta.rosetta.protocols.frags) dump_vd_info() (pyrosetta.rosetta.core.chemical.MutableResidueType method) dump_weights() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) dumpExemplarToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dumpGridToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) DumpPdb (class in pyrosetta.rosetta.protocols.simple_moves) dumpPDB_abinitio (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) dumpPDB_hires (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) dumpPDB_lowres (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) DumpPdbCreator (class in pyrosetta.rosetta.protocols.simple_moves) DumpSingleResidueRotamers (class in pyrosetta.rosetta.protocols.simple_moves) DumpSingleResidueRotamersCreator (class in pyrosetta.rosetta.protocols.simple_moves) dumpTargetPocketsToFile() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) dumpTargetPocketsToPDB() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) DumpTrajectoryEnergy (class in pyrosetta.rosetta.core.energy_methods) DumpTrajectoryEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) dunbrack_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) dunbrack_method (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) DunbrackAAParameterSet (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackConstraint (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackConstraintCreator (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackEnergy (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackEnergyCreator (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_1_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_2_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_3_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_4_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamer_5_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) DunbrackRotamerLibrarySpecificationCreator (class in pyrosetta.rosetta.core.chemical.rotamers) DunbrackRotamerMeanSD_1_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_1_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_2_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_3_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_4_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerMeanSD_5_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackRotamerSampleData (class in pyrosetta.rosetta.core.pack.dunbrack) DunbrackSCSampler (class in pyrosetta.rosetta.protocols.match.upstream) dvect_id_ (pyrosetta.rosetta.core.scoring.hbonds.AssignmentScaleAndDerivVectID property) dvol (pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv property) dw_dr() (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) dWadj_dBase() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj method) dWadj_dWater() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj method) dweight() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) dwell (pyrosetta.rosetta.core.pack.annealer.PointDwell property) dx (pyrosetta.rosetta.core.scoring.APBSResult property) (pyrosetta.rosetta.core.scoring.packstat.LR_AtomData property) (pyrosetta.rosetta.core.scoring.packstat.LR_MP_AtomData property) Dx2y2 (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) 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) Dxy (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) Dxz (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) Dy (pyrosetta.rosetta.core.chemical.element.Elements attribute) dy (pyrosetta.rosetta.core.scoring.APBSResult property) (pyrosetta.rosetta.core.scoring.packstat.LR_AtomData property) (pyrosetta.rosetta.core.scoring.packstat.LR_MP_AtomData property) (pyrosetta.rosetta.numeric.interpolation.spline.Point property) DY3_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) 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_grid_refinement() (pyrosetta.rosetta.protocols.match.MatcherTask method) dynamic_memory_usage() (pyrosetta.rosetta.utility.recent_history_queue method) DynamicAggregateFunction (class in pyrosetta.rosetta.protocols.pack_daemon) DynamicAggregateFunctionDriver (class in pyrosetta.rosetta.protocols.pack_daemon) DynamicIndexRange (class in pyrosetta.rosetta.ObjexxFCL) DynamicProfileThis (class in pyrosetta.rosetta.basic) Dyz (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) dz (pyrosetta.rosetta.core.scoring.APBSResult property) Dz2 (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) 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)