Index – _

_2AX_3EQ_4AX_LINKS (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) _2EQ_3AX_4EQ_LINKS (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) __PyRosetta_instantiate_vector1_MutableResidueType_and_MolFileIOMolecule_types() (in module pyrosetta.rosetta.core.chemical.sdf) _abc_impl (pyrosetta.bindings.pose.PoseResidueAccessor attribute) (pyrosetta.bindings.pose.PoseResidueLabelMaskAccessor attribute) (pyrosetta.bindings.pose.PoseScoreAccessor attribute) (pyrosetta.bindings.pose.ResidueLabelAccessor attribute) (pyrosetta.io.silent_file_map.SilentFileEnergyAccessor attribute) (pyrosetta.io.silent_file_map.SilentFileMap attribute) (pyrosetta.io.silent_file_map.SilentFilePoseAccessor attribute) _abs_tolerance (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) _add_weights_from_file() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) _add_weights_from_stream() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) _addExpectedFailure() (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) _addUnexpectedSuccess() (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) _AE_cdr_detection_failed_ (class in pyrosetta.rosetta.protocols.antibody.grafting) _AE_cdr_undefined_ (class in pyrosetta.rosetta.protocols.antibody.grafting) _AE_grafting_failed_ (class in pyrosetta.rosetta.protocols.antibody.grafting) _AE_invalid_cdr_region_ (class in pyrosetta.rosetta.protocols.antibody.grafting) _AE_json_cdr_detection_failed_ (class in pyrosetta.rosetta.protocols.antibody.grafting) _AE_numbering_failed_ (class in pyrosetta.rosetta.protocols.antibody.grafting) _AE_scs_failed_ (class in pyrosetta.rosetta.protocols.antibody.grafting) _AE_unexpected_region_length_ (class in pyrosetta.rosetta.protocols.antibody.grafting) _asdict() (pyrosetta.CD method) _atom_pair_energy_table() (in module pyrosetta.toolbox.atom_pair_energy) _ATOM_RADIUS (class in pyrosetta.rosetta.core.scoring.sc) _ax (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) _baseAssertEqual() (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) _bx (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) _callCleanup() (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) _callSetUp() (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) _callTearDown() (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) _callTestMethod() (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) _class_cleanups (pyrosetta.tests.bindings.core.test_pose.TestPoseIO attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent attribute) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs attribute) _classSetupFailed (pyrosetta.tests.bindings.core.test_pose.TestPoseIO attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent attribute) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs attribute) _dE_dvars (pyrosetta.rosetta.core.optimization.func_1d property) _deprecate() (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) _deriv_sum (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization property) (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm property) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization property) _diffThreshold (pyrosetta.tests.bindings.core.test_pose.TestPoseIO attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent attribute) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs attribute) _DOT (class in pyrosetta.rosetta.core.scoring.sc) _field_defaults (pyrosetta.CD attribute) _fields (pyrosetta.CD attribute) _formatMessage() (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) _from_iterable() (pyrosetta.bindings.pose.ResidueLabelAccessor class method) _func_to_beat (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization property) (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm property) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization property)

_getAssertEqualityFunc() (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) _hash() (pyrosetta.bindings.pose.ResidueLabelAccessor method) _HashEntry (class in pyrosetta.rosetta.protocols.abinitio) _is_interactive() (in module pyrosetta) _last_accepted_step (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization property) (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm property) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization property) _M_getloc() (pyrosetta.rosetta.std.ios_base method) _M_id() (pyrosetta.rosetta.std.locale.id method) _M_write() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t method) (pyrosetta.rosetta.basic.ComparingTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerToFile method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.std.ostream method) (pyrosetta.rosetta.std.ostringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wostream method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) _make() (pyrosetta.CD class method) _map_string_vector_Real (class in pyrosetta.rosetta.protocols.indexed_structure_store) _map_string_vector_Size (class in pyrosetta.rosetta.protocols.indexed_structure_store) _map_string_vector_vector_Real (class in pyrosetta.rosetta.protocols.indexed_structure_store) _MergableEntries (class in pyrosetta.rosetta.protocols.abinitio) _nonmonotone (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization property) _num_calls (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization property) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization property) _num_linemin_calls (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization property) (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm property) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization property) _open_bz2_compressed() (in module pyrosetta.io.silent_file_map) _open_gzip_compressed() (in module pyrosetta.io.silent_file_map) _pmatch() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) _PROBE (class in pyrosetta.rosetta.core.scoring.sc) _pybind11_conduit_v1_() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.logging_support.PythonLoggingSink.sentry method) (pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider method) (pyrosetta.protocols.h5_structure_store_provider.H5StructureStoreProvider method) (pyrosetta.PythonPyExitCallback method) (pyrosetta.rosetta._xmlNode method) (pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t method) (pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t.sentry method) (pyrosetta.rosetta.basic.citation_manager.AuthorNames method) (pyrosetta.rosetta.basic.citation_manager.Citation method) (pyrosetta.rosetta.basic.citation_manager.CitationCollection method) (pyrosetta.rosetta.basic.citation_manager.CitationCollectionBase method) (pyrosetta.rosetta.basic.citation_manager.CitationCollectionList method) (pyrosetta.rosetta.basic.citation_manager.CitationFormat method) (pyrosetta.rosetta.basic.citation_manager.CitationManager method) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType method) (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor method) (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo method) (pyrosetta.rosetta.basic.ComparingTracer method) (pyrosetta.rosetta.basic.ComparingTracer.sentry method) (pyrosetta.rosetta.basic.database.insert_statement_generator.InsertGenerator method) (pyrosetta.rosetta.basic.database.insert_statement_generator.RowDataBase method) (pyrosetta.rosetta.basic.database.schema_generator.Column method) (pyrosetta.rosetta.basic.database.schema_generator.Constraint method) (pyrosetta.rosetta.basic.database.schema_generator.DbBigInt method) (pyrosetta.rosetta.basic.database.schema_generator.DbDataType method) (pyrosetta.rosetta.basic.database.schema_generator.DbDouble method) (pyrosetta.rosetta.basic.database.schema_generator.DbInteger method) (pyrosetta.rosetta.basic.database.schema_generator.DbReal method) (pyrosetta.rosetta.basic.database.schema_generator.DbText method) (pyrosetta.rosetta.basic.database.schema_generator.DbTextKey method) (pyrosetta.rosetta.basic.database.schema_generator.DbUUID method) (pyrosetta.rosetta.basic.database.schema_generator.ForeignKey method) (pyrosetta.rosetta.basic.database.schema_generator.GreaterThanConstraint method) (pyrosetta.rosetta.basic.database.schema_generator.Index method) (pyrosetta.rosetta.basic.database.schema_generator.PrimaryKey method) (pyrosetta.rosetta.basic.database.schema_generator.Schema method) (pyrosetta.rosetta.basic.database.schema_generator.UniqueConstraint method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableResRotPairFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.CacheableUint64MathMatrixFloatMap method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.ResRotPair method) (pyrosetta.rosetta.basic.datacache.ResRotPairHasher method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataFactory method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.DynamicProfileThis method) (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.gpu.float4 method) (pyrosetta.rosetta.basic.gpu.Timer method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.MemTracer.TracerProxy method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.sentry method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl.sentry method) (pyrosetta.rosetta.basic.MetricValueBase method) (pyrosetta.rosetta.basic.mpi.DbMoverMessageListener method) (pyrosetta.rosetta.basic.mpi.listener_tags method) (pyrosetta.rosetta.basic.mpi.MessageListener method) (pyrosetta.rosetta.basic.mpi.MessageListenerFactory method) (pyrosetta.rosetta.basic.mpi.mpi_tags method) (pyrosetta.rosetta.basic.ProfileThis method) (pyrosetta.rosetta.basic.ProfTag method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.PyTracer.sentry method) (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.sampling.orientations.Permute method) (pyrosetta.rosetta.basic.sampling.orientations.QuatDBMetadata method) (pyrosetta.rosetta.basic.sampling.orientations.Quaternion method) (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGrid method) (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGridManager method) (pyrosetta.rosetta.basic.sampling.orientations.QuatSet method) (pyrosetta.rosetta.basic.sampling.orientations.Triple method) (pyrosetta.rosetta.basic.svd.SVD_Solver method) (pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowManager method) (pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowProtocolBase method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_bool_t method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_double_t method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_float_t method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_int_t method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_long_t method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_unsigned_int_t method) (pyrosetta.rosetta.basic.tensorflow_manager.TFDataTypeDetector_unsigned_long_t method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadAllocation method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManager method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManagerAdvancedAPIKey method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManagerInitializationTracker method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.Tracer.TracerProxy method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.sentry method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl.sentry method) (pyrosetta.rosetta.basic.TracerOptions method) (pyrosetta.rosetta.basic.TracerPriority method) (pyrosetta.rosetta.basic.TracerToFile method) (pyrosetta.rosetta.basic.TracerToFile.sentry method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.core.chemical.AA method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (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.Adduct method) (pyrosetta.rosetta.core.chemical.Ancestor method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomPropertiesManager method) (pyrosetta.rosetta.core.chemical.AtomProperty method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.BondAromaticity method) (pyrosetta.rosetta.core.chemical.BondConjugability method) (pyrosetta.rosetta.core.chemical.BondIsometry method) (pyrosetta.rosetta.core.chemical.BondName method) (pyrosetta.rosetta.core.chemical.BondOrder method) (pyrosetta.rosetta.core.chemical.BondRingness method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.RootData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.core.chemical.ChangeAncestory method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChemicalManager 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.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration.AngularMomentumQuantumNumber method) (pyrosetta.rosetta.core.chemical.ElectronConfiguration.PrincipalQuantumNumber method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.element.Elements method) (pyrosetta.rosetta.core.chemical.Element.Properties method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.GreekDistance method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.Hybridization method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ICoordAtomIDType method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.io.merge_residue_behavior method) (pyrosetta.rosetta.core.chemical.io.MergeAndSplitBehaviorManager method) (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.mmCIF.mmCIFParser method) (pyrosetta.rosetta.core.chemical.modifications.ChemistryBase method) (pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus method) (pyrosetta.rosetta.core.chemical.modifications.Reprotonate method) (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueConnection method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeMapper method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PatchOperationCreator method) (pyrosetta.rosetta.core.chemical.PatchOperationFactory method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype method) (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMol method) (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions method) (pyrosetta.rosetta.core.chemical.RealFilter method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RefConvert_std_string_t method) (pyrosetta.rosetta.core.chemical.RefConvert_unsigned_long_t method) (pyrosetta.rosetta.core.chemical.RefConvert_void__star__t 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.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueDatabaseIO method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperty method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) (pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation method) (pyrosetta.rosetta.core.chemical.rings.CPParameter method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) (pyrosetta.rosetta.core.chemical.rings.RingSaturationType method) (pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation method) (pyrosetta.rosetta.core.chemical.rna.BaseEdge method) (pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide method) (pyrosetta.rosetta.core.chemical.rna.ChiState method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation method) (pyrosetta.rosetta.core.chemical.rna.PuckerState method) (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion method) (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.sdf.BondData method) (pyrosetta.rosetta.core.chemical.sdf.CtabParserBase method) (pyrosetta.rosetta.core.chemical.sdf.CtabV2000Parser method) (pyrosetta.rosetta.core.chemical.sdf.CtabV3000Parser method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader method) (pyrosetta.rosetta.core.chemical.sdf.MolWriter method) (pyrosetta.rosetta.core.chemical.sdf.SDFParser 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) (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.TypeSetMode method) (pyrosetta.rosetta.core.chemical.VariantType method) (pyrosetta.rosetta.core.chemical.VDDistanceMatrix method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) (pyrosetta.rosetta.core.conformation.AbstractRotamerTrie method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.AtomGraphEdgeData method) (pyrosetta.rosetta.core.conformation.AtomGraphVertexData method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.ConformationKinWriter method) (pyrosetta.rosetta.core.conformation.DefaultCubeHash method) (pyrosetta.rosetta.core.conformation.ExactResidueMatcher method) (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) (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.conformation.membrane.ImplicitLipidInfo method) (pyrosetta.rosetta.core.conformation.membrane.MEM method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION method) (pyrosetta.rosetta.core.conformation.membrane.Orientation method) (pyrosetta.rosetta.core.conformation.membrane.Span method) (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) (pyrosetta.rosetta.core.conformation.orbitals.OrbitalXYZCoords method) (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.ParameterizationCalculatorProperties method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.parametric.ParameterType method) (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType 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.conformation.PointGraphEdgeData method) (pyrosetta.rosetta.core.conformation.PointGraphPy method) (pyrosetta.rosetta.core.conformation.PointGraphVertexData method) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin method) (pyrosetta.rosetta.core.conformation.PseudoBond method) (pyrosetta.rosetta.core.conformation.PseudoBondCollection method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.residue_datacache.ResidueDataCacheIndex method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) (pyrosetta.rosetta.core.conformation.ResidueMatcher method) (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.Strategy method) (pyrosetta.rosetta.core.conformation.symmetry.dof_type method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType method) (pyrosetta.rosetta.core.conformation.symmetry.SlideType method) (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoader method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform method) (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) (pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate method) (pyrosetta.rosetta.core.conformation.UltraLightResidue method) (pyrosetta.rosetta.core.conformation.WatsonCrickResidueMatcher method) (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AACompositionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.AbegoEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAllCreator method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAroCreator method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDensCreator method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) (pyrosetta.rosetta.core.energy_methods.GridInfo method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.energy_methods.ImplicitMembraneCoulomb method) (pyrosetta.rosetta.core.energy_methods.ImplicitMembraneElecEnergy method) (pyrosetta.rosetta.core.energy_methods.ImplicitMembraneElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_hackCreator method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenaltiesCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MembraneLipoCreator method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebodyCreator method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PoseSequence method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.ProQ_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2BCreator method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonicalCreator method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_RohlCreator method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_FastCreator method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNACreator method) (pyrosetta.rosetta.core.energy_methods.RG_Local_MinData method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RG_MinData method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RMS_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphateCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCreatorCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCreatorFA method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.ScoreCache method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterWeightGridSet method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergyCreator method) (pyrosetta.rosetta.core.environment.DofPassport method) (pyrosetta.rosetta.core.environment.EnvCore method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.environment.FoldTreeSketch method) (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) (pyrosetta.rosetta.core.environment.LocalPosition method) (pyrosetta.rosetta.core.environment.SequenceAnnotation method) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType method) (pyrosetta.rosetta.core.enzymes.EnzymeData method) (pyrosetta.rosetta.core.enzymes.EnzymeManager method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BaseCacheUnit method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.CacheWrapper_protocols_simple_moves_GunnTuple_core_fragment_MapCacheUnit_protocols_simple_moves_GunnTuple_t method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSetIterator_ method) (pyrosetta.rosetta.core.fragment.ConstFrameIterator method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragCache_protocols_simple_moves_GunnTuple_t method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.FragFactory method) (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.core.fragment.FragID_Iterator method) (pyrosetta.rosetta.core.fragment.FragmentIO method) (pyrosetta.rosetta.core.fragment.FragmentRmsd method) (pyrosetta.rosetta.core.fragment.FragmentSetLoader method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.FrameIterator method) (pyrosetta.rosetta.core.fragment.FrameIteratorWorker_ method) (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.FrameListIterator_ method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.MinimalFragSetIterator_ method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSetIterator_ method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Book_core_fragment_picking_old_vall_VallResidues_t method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Book_VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_core_fragment_picking_old_vall_VallSections_t method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.fragment.rna._RNA_MatchType_ method) (pyrosetta.rosetta.core.fragment.rna.FragmentLibrary method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.RNA_FragmentHomologyExclusion method) (pyrosetta.rosetta.core.fragment.rna.RNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.core.fragment.rna.TorsionSet method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.torsions method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (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.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.BondID method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID 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.DOF_ID_Range method) (pyrosetta.rosetta.core.id.DOF_Type method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.MainchainTorsionType method) (pyrosetta.rosetta.core.id.NamedAtomID 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.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.PartialAtomID method) (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.id.TorsionType method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.import_pose.FileType method) (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) (pyrosetta.rosetta.core.import_pose.libraries.BasePairType method) (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) (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.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.pose_stream.ExtendedPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.LazySilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.MetaPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.PoseResource method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoader method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator method) (pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.core.import_pose.RNA_JumpMover method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.CrystInfo method) (pyrosetta.rosetta.core.io.external.PsiPredInterface method) (pyrosetta.rosetta.core.io.external.PsiPredResult method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.mmtf.ai_cmp method) (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum method) (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager method) (pyrosetta.rosetta.core.io.mmtf.sd_index method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.nmr.AtomSelection method) (pyrosetta.rosetta.core.io.nmr.ParaIon method) (pyrosetta.rosetta.core.io.nmr.ParamagneticDatabaseHandler method) (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseHandler method) (pyrosetta.rosetta.core.io.NomenclatureManager method) (pyrosetta.rosetta.core.io.pdb.Field method) (pyrosetta.rosetta.core.io.pdb.RecordCollection method) (pyrosetta.rosetta.core.io.pdb.RecordType method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData 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.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.NumberingSystem method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.ResNum method) (pyrosetta.rosetta.core.io.raw_data.RawFileData 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.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreMap method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique method) (pyrosetta.rosetta.core.io.RemarkInfo method) (pyrosetta.rosetta.core.io.Remarks method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.serialization.BUFFER method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.EnergyNames method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SharedSilentData method) (pyrosetta.rosetta.core.io.silent.SharedSilentDataType method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileData.iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine method) (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) (pyrosetta.rosetta.core.io.silent.SimpleSequenceData method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtom method) (pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray method) (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms method) (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry method) (pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure method) (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.jacobian_struct method) (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.screw_construct_struct method) (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians method) (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobianTypeEnum method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.MinimizerMapBase method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.RT method) (pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree method) (pyrosetta.rosetta.core.kinematics.Stub 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.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.CMAES_Minimizer method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DescentDirectionAlgorithm method) (pyrosetta.rosetta.core.optimization.DFPMinConvergedAbsolute method) (pyrosetta.rosetta.core.optimization.DFPMinConvergedFractional method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.optimization.EItem method) (pyrosetta.rosetta.core.optimization.func_1d method) (pyrosetta.rosetta.core.optimization.GA_Minimizer method) (pyrosetta.rosetta.core.optimization.JJH_Minimizer method) (pyrosetta.rosetta.core.optimization.lbfgs_iteration_data method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.MinimizerOptions method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.NelderMeadSimplex method) (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.NumericalDerivCheckResult method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.annealer.AnnealerFactory method) (pyrosetta.rosetta.core.pack.annealer.AnnealerObserver method) (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.PointDwell method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotSub method) (pyrosetta.rosetta.core.pack.annealer.SeqSymmAnnealerSetup method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergyCreator method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator method) (pyrosetta.rosetta.core.pack.dunbrack.ChiSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.MainchainTorsionReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PeptideTorsionReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptoidGeneralDOFReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptoidOmegaReporter method) (pyrosetta.rosetta.core.pack.dunbrack.ProbSortClass method) (pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenaltyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.HBondBonusOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ReweightData method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.UnsatCorrectionOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomeHelper method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.MyWaterHolder method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.BlockParam method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.MyTemplatePointerHash1_core_conformation_Residue_t method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.RotamerRotamerHasher method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.exposed_hydrophobic_data method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergyCreator method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphFactory method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsRadiusData method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergyCreator method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.core.pack.palette.BaseTypeList method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelector method) (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelectorDecision method) (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator method) (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerCouplings method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetFactory method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsFactory method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory method) (pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy method) (pyrosetta.rosetta.core.pack.RTMin method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMultifunc method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.ExtraRotSample method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) (pyrosetta.rosetta.core.pack.task.IGEdgeReweighter method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilter method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilter method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIs method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamerSamplingData method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilter method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.OptHCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReplicateTask method) (pyrosetta.rosetta.core.pack.task.operation.ResFilter method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs.ChainPos method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt.ChainPos method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilter method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesignCreator method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosionCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplings method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplingsCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinks method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinksCreator method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.PackerTaskSymmetryStatus method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.ResfileContents method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelectorCreator method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.core.pose.copydofs.CopyDofs method) (pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo method) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType method) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.CalculatorFactory method) (pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDeltaEnergeticsCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceNeighborDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceSasaDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculator2 method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculatorLegacy method) (pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBInfo.AtomRecord method) (pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose method) (pyrosetta.rosetta.core.pose.RID_FileSource method) (pyrosetta.rosetta.core.pose.RID_Source method) (pyrosetta.rosetta.core.pose.rna.Atom_Bin method) (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BasePairStep method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_Datum method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_Reactivity method) (pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType method) (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.pose.rna.StubStubType method) (pyrosetta.rosetta.core.pose.rna.Terminus method) (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose.const_iterator method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose.iter_base_numeric_geometry_hashing_xyzStripeHash_const_iterator_t method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.annealing.ResidueArrayAnnealableEnergy method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM method) (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.atomic_depth.AtomicDepth method) (pyrosetta.rosetta.core.scoring.atomic_depth.point3d method) (pyrosetta.rosetta.core.scoring.atomic_depth.volumepixel method) (pyrosetta.rosetta.core.scoring.atomic_depth.voxel method) (pyrosetta.rosetta.core.scoring.atomic_depth.voxel2 method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.AtomVDW method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculatorManager method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES method) (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergyCreator method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondPotential method) (pyrosetta.rosetta.core.scoring.CenHBPotential method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.CenRotEnvPairPotential method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator 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.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintFactory method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergyCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.constraints.CstMinimizationData method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator 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.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Obsolet_NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints 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.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.constraints.XYZs method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.ContextGraphFactory method) (pyrosetta.rosetta.core.scoring.ContextGraphType method) (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.atoms_and_func_struct method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergyCreator method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.resatom_and_func_struct method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DC.DC_TYPE method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DensityZscoresStatsSetup method) (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.core.scoring.DipolarCoupling 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.CentroidDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingDatabase method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyComponents method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.RT_helper method) (pyrosetta.rosetta.core.scoring.disulfides.SG_Dist_Func method) (pyrosetta.rosetta.core.scoring.disulfides.SGSG_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) (pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential method) (pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential method) (pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential method) (pyrosetta.rosetta.core.scoring.dna.DNABFormPotential method) (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) (pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.Pairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative method) (pyrosetta.rosetta.core.scoring.elec.ElecGroup method) (pyrosetta.rosetta.core.scoring.elec.electrie.ElecAtom method) (pyrosetta.rosetta.core.scoring.elec.electrie.ElecTrieEvaluator method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator method) (pyrosetta.rosetta.core.scoring.elec.GroupElec method) (pyrosetta.rosetta.core.scoring.elec.weight_triple method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.electron_density.poseCoord method) (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.EnvPairPotential method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) (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) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy 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.coulomb.Coulomb method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairAll method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFactory method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairNone method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CPCrossoverBehavior method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CPResidueConnectionType method) (pyrosetta.rosetta.core.scoring.etable.count_pair.Invoker method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableClassicIntraEnergyCreator method) (pyrosetta.rosetta.core.scoring.etable.EtableEnergyCreator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableOptions method) (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_1 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_2 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_3 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairDataGeneric method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom method) (pyrosetta.rosetta.core.scoring.etable.etrie.GenericResidueConnectionData method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPair1BC3 method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPair1BC4 method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairAll method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairNone method) (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.ExcludedResPredicate method) (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSPotential method) (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeMap method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffraction method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.Hankel method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering 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.ConformationXYZ 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.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.FuncFactory 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.ResiduePairXYZ method) (pyrosetta.rosetta.core.scoring.func.ResidueXYZ 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.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.GenBondedExclInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Hairpins method) (pyrosetta.rosetta.core.scoring.hbonds.AssignmentScaleAndDerivVectID method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.LKHBondInfo method) (pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) (pyrosetta.rosetta.core.scoring.hbonds.HBDerivType method) (pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType method) (pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple method) (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType method) (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType method) (pyrosetta.rosetta.core.scoring.hbonds.HBond method) (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) (pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergyCreator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager method) (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType method) (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBCountPairFunction method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBCPData method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters method) (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.HydroxylTorsionPotential method) (pyrosetta.rosetta.core.scoring.interface_.DDPlookup method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.interface_.DDPscoreCreator method) (pyrosetta.rosetta.core.scoring.IsHeavyAtomPredicate method) (pyrosetta.rosetta.core.scoring.IsMainAtomPredicate method) (pyrosetta.rosetta.core.scoring.IsProteinBackboneIncludingOPredicate method) (pyrosetta.rosetta.core.scoring.IsProteinBackbonePredicate method) (pyrosetta.rosetta.core.scoring.IsProteinCAPredicate method) (pyrosetta.rosetta.core.scoring.IsSpecificAtomsPredicate method) (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergyCreator method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergyCreator method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBAtom method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBTrieEvaluator method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.ScoredBridgingWater method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotential method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle method) (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.magnesium.MgKnowledgeBasedPotential method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters 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.dfire.DFIRE_Potential method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethods method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType method) (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInterCreator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntraCreator method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NeighborListData method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.PyEnergyMethodRegistrator method) (pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps 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.mhc_epitope_energy.AlleleMatrix method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM method) (pyrosetta.rosetta.core.scoring.min_pair_data method) (pyrosetta.rosetta.core.scoring.min_single_data method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMBondLengthLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMBondLengthScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionScore method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) (pyrosetta.rosetta.core.scoring.motif.MotifHit method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.MotifHitStats method) (pyrosetta.rosetta.core.scoring.motif.MotifMatchOverlapReq method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.scoring.motif.RM_Type method) (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats method) (pyrosetta.rosetta.core.scoring.motif.RPM_Type method) (pyrosetta.rosetta.core.scoring.motif.XformScore method) (pyrosetta.rosetta.core.scoring.motif.XformSummary method) (pyrosetta.rosetta.core.scoring.motif.Xfrag method) (pyrosetta.rosetta.core.scoring.motif.XfragSet method) (pyrosetta.rosetta.core.scoring.motif.Xfres method) (pyrosetta.rosetta.core.scoring.MultipoleAxisType method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MultipoleParameter method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.TailFunction method) (pyrosetta.rosetta.core.scoring.nmr.EULER_CONVENTION method) (pyrosetta.rosetta.core.scoring.nmr.NMR_VALUE_AVERAGING_TYPE method) (pyrosetta.rosetta.core.scoring.nmr.NMRDataFactory method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid method) (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel.CONFORMER_FILTER method) (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet.COMPUTATION_TYPE method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) (pyrosetta.rosetta.core.scoring.nmr.PRE_RATE_TYPE method) (pyrosetta.rosetta.core.scoring.nmr.PRE_SPIN_TYPE method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet.COMPUTATION_TYPE method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) (pyrosetta.rosetta.core.scoring.nmr.RDC_NORM_TYPE method) (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE method) (pyrosetta.rosetta.core.scoring.nmr.SINGLE_NMR_VALUE_WEIGHTING method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA method) (pyrosetta.rosetta.core.scoring.nv.NVlookup method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.nv.NVscoreCreator method) (pyrosetta.rosetta.core.scoring.OmegaTether method) (pyrosetta.rosetta.core.scoring.OneDDistPotential method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup.h_type method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScoreCreator method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name method) (pyrosetta.rosetta.core.scoring.P_AA method) (pyrosetta.rosetta.core.scoring.P_AA_ABEGO3 method) (pyrosetta.rosetta.core.scoring.P_AA_ss method) (pyrosetta.rosetta.core.scoring.packing.Ball method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.packing.HolesParams method) (pyrosetta.rosetta.core.scoring.packing.HolesParamsRes method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.packing.PoseBallsLite method) (pyrosetta.rosetta.core.scoring.packing.SurfVol method) (pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv method) (pyrosetta.rosetta.core.scoring.packstat.Accumulator method) (pyrosetta.rosetta.core.scoring.packstat.AreaAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.Array2D method) (pyrosetta.rosetta.core.scoring.packstat.AtomRadiusMap method) (pyrosetta.rosetta.core.scoring.packstat.CavityBall method) (pyrosetta.rosetta.core.scoring.packstat.CavityBallCluster method) (pyrosetta.rosetta.core.scoring.packstat.Circle method) (pyrosetta.rosetta.core.scoring.packstat.Event method) (pyrosetta.rosetta.core.scoring.packstat.EventType method) (pyrosetta.rosetta.core.scoring.packstat.LeeRichards method) (pyrosetta.rosetta.core.scoring.packstat.LR_AtomData method) (pyrosetta.rosetta.core.scoring.packstat.LR_MP_AtomData method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.Octree2D method) (pyrosetta.rosetta.core.scoring.packstat.OrderCBC method) (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) (pyrosetta.rosetta.core.scoring.packstat.PackingScoreResData method) (pyrosetta.rosetta.core.scoring.packstat.PerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.Point method) (pyrosetta.rosetta.core.scoring.packstat.PointPair method) (pyrosetta.rosetta.core.scoring.packstat.PosePackData method) (pyrosetta.rosetta.core.scoring.packstat.SasaOptions method) (pyrosetta.rosetta.core.scoring.packstat.SasaResult method) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom method) (pyrosetta.rosetta.core.scoring.packstat.Slice method) (pyrosetta.rosetta.core.scoring.packstat.Sphere method) (pyrosetta.rosetta.core.scoring.packstat.trace method) (pyrosetta.rosetta.core.scoring.PairEPotential method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PDinter method) (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.PointWaterPotential method) (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.ProQPotential method) (pyrosetta.rosetta.core.scoring.ProteinTorsion method) (pyrosetta.rosetta.core.scoring.Rama_Table_Type method) (pyrosetta.rosetta.core.scoring.Ramachandran method) (pyrosetta.rosetta.core.scoring.Ramachandran2B method) (pyrosetta.rosetta.core.scoring.RamaPrePro method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC.RDC_TYPE method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling_Rohl method) (pyrosetta.rosetta.core.scoring.ResidueExclParams method) (pyrosetta.rosetta.core.scoring.ResidueNblistData method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResiduePairNeighborList method) (pyrosetta.rosetta.core.scoring.ResPairMinimizationData method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResSingleMinimizationData method) (pyrosetta.rosetta.core.scoring.rmsd_atoms method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) (pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotentialCreator method) (pyrosetta.rosetta.core.scoring.rna.RNA_Motif method) (pyrosetta.rosetta.core.scoring.rna.RNA_Motifs method) (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_SuitePotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) (pyrosetta.rosetta.core.scoring.rna.RNP_LowResStackData method) (pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential method) (pyrosetta.rosetta.core.scoring.SAnode method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethodEnum method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode method) (pyrosetta.rosetta.core.scoring.sasa.SasaRadii method) (pyrosetta.rosetta.core.scoring.SASAPotential method) (pyrosetta.rosetta.core.scoring.saxs.DistanceHistogram method) (pyrosetta.rosetta.core.scoring.saxs.FormFactor method) (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) (pyrosetta.rosetta.core.scoring.saxs.SinXOverX method) (pyrosetta.rosetta.core.scoring.sc._ATOM_RADIUS method) (pyrosetta.rosetta.core.scoring.sc._DOT method) (pyrosetta.rosetta.core.scoring.sc._PROBE method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityResults method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityResults method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) (pyrosetta.rosetta.core.scoring.ScoreFunctionKey method) (pyrosetta.rosetta.core.scoring.ScoreType method) (pyrosetta.rosetta.core.scoring.ScoreTypeManager method) (pyrosetta.rosetta.core.scoring.ScoringManager method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SelectedResPredicate method) (pyrosetta.rosetta.core.scoring.SmallAtNb method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.SplitUnfoldedTwoBodyPotential method) (pyrosetta.rosetta.core.scoring.SpringParams method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.sym_e.symECreator method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.tableID method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TMscore method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.TorsionParams method) (pyrosetta.rosetta.core.scoring.trie.CPDataCorrespondence method) (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) (pyrosetta.rosetta.core.scoring.trie.TrieCollection method) (pyrosetta.rosetta.core.scoring.trie.TrieCountPairBase method) (pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_EnergyCreator method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieCountPair1B method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.select.Enumerate1WithSelector method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator method) (pyrosetta.rosetta.core.select.movemap.move_map_action method) (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) (pyrosetta.rosetta.core.select.PreSelectedResidRange method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.basic_selection_logic method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelector method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.slice_enums.OutOfBoundsMode method) (pyrosetta.rosetta.core.select.residue_selector.slice_enums.SliceMode method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector.SSElement method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.Aligner method) (pyrosetta.rosetta.core.sequence.AlignerFactory method) (pyrosetta.rosetta.core.sequence.AlignMove method) (pyrosetta.rosetta.core.sequence.AnnotatedSequence method) (pyrosetta.rosetta.core.sequence.Blosum62Map method) (pyrosetta.rosetta.core.sequence.Cell method) (pyrosetta.rosetta.core.sequence.CharPairHash method) (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequenceCreator method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequenceCreator method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.DP_Matrix method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.MCAligner method) (pyrosetta.rosetta.core.sequence.NWAligner method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringSchemeFactory method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.core.sequence.SequenceAlignmentHasher method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceCouplingCreator method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.core.sequence.SequenceFactory method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.core.sequence.SequenceProfileCreator method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) (pyrosetta.rosetta.core.sequence.SimpleSequenceCreator method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SWAligner method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetricCreator 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.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.MetricKey method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueBfactorMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueBfactorMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator method) (pyrosetta.rosetta.core.util.ChainbreakUtil method) (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.result.next_row method) (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.backend.statements_cache method) (pyrosetta.rosetta.cppdb.connection_info method) (pyrosetta.rosetta.cppdb.connection_specific_data method) (pyrosetta.rosetta.cppdb.pool method) (pyrosetta.rosetta.cppdb.ref_counted 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.cppdb.result method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.cppdb.statement method) (pyrosetta.rosetta.cppdb.transaction method) (pyrosetta.rosetta.numeric.AgglomerativeHierarchicalClusterer method) (pyrosetta.rosetta.numeric.alignment.QCPKernel_double_t method) (pyrosetta.rosetta.numeric.AverageLinkClusterer method) (pyrosetta.rosetta.numeric.AxisRotationSampler method) (pyrosetta.rosetta.numeric.Calculator method) (pyrosetta.rosetta.numeric.ClusteringTreeNode method) (pyrosetta.rosetta.numeric.ClusterOptions method) (pyrosetta.rosetta.numeric.CompleteLinkClusterer method) (pyrosetta.rosetta.numeric.conversions.AngleUnit method) (pyrosetta.rosetta.numeric.CubicPolynomial method) (pyrosetta.rosetta.numeric.DiscreteIntervalEncodingTree_unsigned_long_t method) (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.ArithmeticASTAndClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTOrClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTTerm method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticScanner method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.BinaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionScanner 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.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.FunctionToken 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.LiteralToken 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.SimpleExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.SimpleToken method) (pyrosetta.rosetta.numeric.expression_parser.SquarerootExpression method) (pyrosetta.rosetta.numeric.expression_parser.SubtractExpression method) (pyrosetta.rosetta.numeric.expression_parser.Token method) (pyrosetta.rosetta.numeric.expression_parser.TokenSet method) (pyrosetta.rosetta.numeric.expression_parser.TokenType method) (pyrosetta.rosetta.numeric.expression_parser.UnaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.VariableExpression method) (pyrosetta.rosetta.numeric.expression_parser.VariableToken method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fft_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.fourier.SHT method) (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.Ball method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.geometry.hashing.Counter method) (pyrosetta.rosetta.numeric.geometry.hashing.MinimalClashHash method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash.const_iterator method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash.iter_base_numeric_geometry_hashing_xyzStripeHash_const_iterator_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float_t method) (pyrosetta.rosetta.numeric.histograms.TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (pyrosetta.rosetta.numeric.interpolation.CatmullRomSplineBoundaryType method) (pyrosetta.rosetta.numeric.interpolation.HistogramCOP_double_double_t method) (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.BorderFlag method) (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.interp_range method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.LinearFunction method) (pyrosetta.rosetta.numeric.interpolation.spline.Point method) (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.interpolation.spline.SimpleInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) (pyrosetta.rosetta.numeric.IntervalSet_Double method) (pyrosetta.rosetta.numeric.IntervalSet_double_t method) (pyrosetta.rosetta.numeric.IOTraits_double_t method) (pyrosetta.rosetta.numeric.IOTraits_float_t method) (pyrosetta.rosetta.numeric.IOTraits_int_t method) (pyrosetta.rosetta.numeric.IOTraits_long_double_t method) (pyrosetta.rosetta.numeric.IOTraits_long_t method) (pyrosetta.rosetta.numeric.IOTraits_short_t method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_int_t method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_long_t method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_short_t method) (pyrosetta.rosetta.numeric.kdtree.CompareKDPoints method) (pyrosetta.rosetta.numeric.kdtree.HyperRectangle method) (pyrosetta.rosetta.numeric.kdtree.KDNode method) (pyrosetta.rosetta.numeric.kdtree.KDPoint method) (pyrosetta.rosetta.numeric.kdtree.KDPoint_MinDist method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.kdtree.KDTree method) (pyrosetta.rosetta.numeric.kinematic_closure.p method) (pyrosetta.rosetta.numeric.linear_algebra.EllipseParameters method) (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t 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) (pyrosetta.rosetta.numeric.MathTensor_double_t method) (pyrosetta.rosetta.numeric.MathVector_double_t method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.numeric.ModSelector_long_true_t method) (pyrosetta.rosetta.numeric.ModSelector_unsigned_long_true_t method) (pyrosetta.rosetta.numeric.ModuloSelector_double_false_t method) (pyrosetta.rosetta.numeric.ModuloSelector_int_true_t method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.nls.lm_control_struct method) (pyrosetta.rosetta.numeric.nls.lm_status_struct method) (pyrosetta.rosetta.numeric.NumericTraits_double_t method) (pyrosetta.rosetta.numeric.NumericTraits_float_t method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t method) (pyrosetta.rosetta.numeric.Polynomial_1d method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.random.mt19937_RG method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) (pyrosetta.rosetta.numeric.random.WeightedSampler method) (pyrosetta.rosetta.numeric.RemainderSelector_double_false_t method) (pyrosetta.rosetta.numeric.RemainderSelector_int_true_t method) (pyrosetta.rosetta.numeric.RocCurve method) (pyrosetta.rosetta.numeric.RocPoint method) (pyrosetta.rosetta.numeric.RocStatus method) (pyrosetta.rosetta.numeric.SingleLinkClusterer method) (pyrosetta.rosetta.numeric.SplineParameters method) (pyrosetta.rosetta.numeric.UniformRotationSampler method) (pyrosetta.rosetta.numeric.urs_Quat method) (pyrosetta.rosetta.numeric.XformHash32 method) (pyrosetta.rosetta.numeric.XformHash64 method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t 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.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ChunkExponent method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (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.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) 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(pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_bool_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_char_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_double_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_float_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_int_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_long_double_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_long_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_ObjexxFCL_byte_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_ObjexxFCL_Fstring_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_short_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_signed_char_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_std_complex_float_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_std_complex_long_double_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.format.Bite_unsigned_short_t method) (pyrosetta.rosetta.ObjexxFCL.format.Skip method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.internal.InitializerSentinel method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.ObjexxFCL.internal.ProxySentinel method) (pyrosetta.rosetta.ObjexxFCL.ModSelector_int_true_t method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.ObjexxFCL.Star method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_double_t method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_float_t method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_int_t method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_long_double_t method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_long_t method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_short_t method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_short_t method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.abinitio._HashEntry method) (pyrosetta.rosetta.protocols.abinitio._MergableEntries method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMoverCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleDataCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.StageID method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCMCreator method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.AlternativePairings method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax.IterationStage method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid.IterationStage method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom.IterationStage method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio.StageID method) (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.abinitio.StageID method) (pyrosetta.rosetta.protocols.abinitio.StrandConstraints method) (pyrosetta.rosetta.protocols.abinitio.Template method) (pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.Templates method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetricCreator method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMoverCreator method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.InterfaceRegion method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafterCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumbering method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMoverCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum method) (pyrosetta.rosetta.protocols.antibody.CDRDBPose method) (pyrosetta.rosetta.protocols.antibody.CDRDBSequence method) (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum method) (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum method) (pyrosetta.rosetta.protocols.antibody.CDRNameEnum method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocolEnum method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum method) (pyrosetta.rosetta.protocols.antibody.design.MutantPosition method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector method) (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum method) (pyrosetta.rosetta.protocols.antibody.FrameWork method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer 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.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyNumbering method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3BaseTypeEnum method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.LightChainTypeEnum method) (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum method) (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_double_t method) (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_long_t method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMoverCreator method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPreProCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMoverCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocolCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMoverCreator method) (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2Creator method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) (pyrosetta.rosetta.protocols.buns.CALCULATORMODE method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoidsFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.OperatorFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2.ScoreType method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2Creator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeightFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_filters.SigmoidFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder.Frame method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.InterpolationType method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer 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.canonical_sampling.mc_convergence_checks.Heat_ConvergenceCheck method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_ConvergenceCheck method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_Evaluator method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.PoolData method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec method) (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpecStyle method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.QuenchDirection method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator method) (pyrosetta.rosetta.protocols.cartesian.CartesianAtom method) (pyrosetta.rosetta.protocols.cartesian.MD_Angle method) (pyrosetta.rosetta.protocols.cartesian.MD_Bond method) (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral method) (pyrosetta.rosetta.protocols.cartesian.MolecularDynamics method) (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) (pyrosetta.rosetta.protocols.checkpoint.FileBuffer method) (pyrosetta.rosetta.protocols.checkpoint.Timer method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMoverCreator method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.ChemistryCreator method) (pyrosetta.rosetta.protocols.chemistries.ChemistryFactory method) (pyrosetta.rosetta.protocols.chemistries.ChemistryLoader method) (pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator method) (pyrosetta.rosetta.protocols.chemistries.ReprotonateChemistry method) (pyrosetta.rosetta.protocols.chemistries.ReprotonateCreator method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) (pyrosetta.rosetta.protocols.chromophore.ChromophoreDataReader method) (pyrosetta.rosetta.protocols.chromophore.ReadResidueCoordinatesFromPDB method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.calibur.ADJ_LIST_MODE method) (pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList method) (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) (pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE method) (pyrosetta.rosetta.protocols.cluster.calibur.INPUT_FILE_TYPE method) (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB method) (pyrosetta.rosetta.protocols.cluster.calibur.SimPDB method) (pyrosetta.rosetta.protocols.cluster.calibur.Stru method) (pyrosetta.rosetta.protocols.cluster.Cluster method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.DataPoint method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.Exemplar method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.features.ResidueFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.ResidueFeatureFactory method) (pyrosetta.rosetta.protocols.comparative_modeling.features.SSFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.SSType method) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionBin method) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constel.ChainTerm method) (pyrosetta.rosetta.protocols.constel.ExcludedFilter method) (pyrosetta.rosetta.protocols.constel.FilterByAmphetamine method) (pyrosetta.rosetta.protocols.constel.FilterByHistamine method) (pyrosetta.rosetta.protocols.constel.FilterByIndoleCOO method) (pyrosetta.rosetta.protocols.constel.FilterByProxTerm method) (pyrosetta.rosetta.protocols.constel.FilterBySASA method) (pyrosetta.rosetta.protocols.constel.FilterByTryptamine method) (pyrosetta.rosetta.protocols.constel.HBondCommon method) (pyrosetta.rosetta.protocols.constel.MasterFilter method) (pyrosetta.rosetta.protocols.constel.NeighTeller method) (pyrosetta.rosetta.protocols.constel.OrientCommon method) (pyrosetta.rosetta.protocols.constel.PresenceCommon method) (pyrosetta.rosetta.protocols.constel.ResidueMask method) (pyrosetta.rosetta.protocols.constel.ResMut method) (pyrosetta.rosetta.protocols.constel.SingResCnlCrea method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilterCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator.MappedAtom method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover.AtomSelector method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.contact_map.ContactMapCreator method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocolCreator method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.CrystRMSCreator method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMoverCreator method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfoCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMoverCreator method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroupSetting method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomainCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Lanthionine_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_Metal method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverMode method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PSM_StubMode method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) (pyrosetta.rosetta.protocols.ddG.ddGData method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.SecStructInfo method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.calculators.CavityCalculator method) (pyrosetta.rosetta.protocols.denovo_design.components.Alias method) (pyrosetta.rosetta.protocols.denovo_design.components.BondInfo method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t 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.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing.PairingType method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing.PairingType method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts.SegmentType method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.SolutionPredicate method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing.PairingType method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureSlice method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.connection.AreConnectablePredicate method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.CutAndJump method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNACreator method) (pyrosetta.rosetta.protocols.dna.DNABase method) (pyrosetta.rosetta.protocols.dna.DNABasepair method) (pyrosetta.rosetta.protocols.dna.DNABasestep method) (pyrosetta.rosetta.protocols.dna.DnaChains method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMoverCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePackerCreator method) (pyrosetta.rosetta.protocols.dna.DnaNeighbor method) (pyrosetta.rosetta.protocols.dna.DNAParameters method) (pyrosetta.rosetta.protocols.dna.DnaPosition method) (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.dna.PositionType method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator method) (pyrosetta.rosetta.protocols.dna.ResTypeSequence_lt method) (pyrosetta.rosetta.protocols.dna.RotamerDNAHBondFilter method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDnaCreator method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplings method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator method) (pyrosetta.rosetta.protocols.docking.DHR_Type method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockMinMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMoverCreator method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.docking.RigidBodyInfo method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.TemperedDockingCreator method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.AtomExistsFilter method) (pyrosetta.rosetta.protocols.drug_design.AtomExistsFilterCreator method) (pyrosetta.rosetta.protocols.drug_design.AtomSubstitution method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLReferenceSDFilesManager method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLSampleConfsManager method) (pyrosetta.rosetta.protocols.drug_design.ChemicalReaction method) (pyrosetta.rosetta.protocols.drug_design.ConformationSelectionToRDMol method) (pyrosetta.rosetta.protocols.drug_design.DrugDesignMover method) (pyrosetta.rosetta.protocols.drug_design.DrugDesignMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.DrugPolishMover method) (pyrosetta.rosetta.protocols.drug_design.DrugPolishMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter method) (pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilterCreator method) (pyrosetta.rosetta.protocols.drug_design.LigandLocationFilter method) (pyrosetta.rosetta.protocols.drug_design.LigandLocationFilterCreator method) (pyrosetta.rosetta.protocols.drug_design.MoleculeSelection method) (pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution method) (pyrosetta.rosetta.protocols.drug_design.NChiFilter method) (pyrosetta.rosetta.protocols.drug_design.NChiFilterCreator method) (pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand method) (pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigandCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilterCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler method) (pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler.Product method) (pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler.Product.HashFunction method) (pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler.Reagent method) (pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSamplerCreator method) (pyrosetta.rosetta.protocols.drug_design.ReactionChemistry method) (pyrosetta.rosetta.protocols.drug_design.ReactionFragment method) (pyrosetta.rosetta.protocols.drug_design.ReactionFragmentCreator method) (pyrosetta.rosetta.protocols.drug_design.ReactionGrow method) (pyrosetta.rosetta.protocols.drug_design.ReactionGrowCreator method) (pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransform method) (pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransformCreator method) (pyrosetta.rosetta.protocols.drug_design.SAScoreData method) (pyrosetta.rosetta.protocols.drug_design.SAScoreFilter method) (pyrosetta.rosetta.protocols.drug_design.SAScoreFilterCreator method) (pyrosetta.rosetta.protocols.drug_design.SubstituentReplace method) (pyrosetta.rosetta.protocols.drug_design.SubstituentReplaceCreator method) (pyrosetta.rosetta.protocols.drug_design.SubstructureReplace method) (pyrosetta.rosetta.protocols.drug_design.SubstructureReplaceCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions method) (pyrosetta.rosetta.protocols.electron_density.PerlinNoise method) (pyrosetta.rosetta.protocols.electron_density.PointScoreComparator method) (pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions method) (pyrosetta.rosetta.protocols.electron_density.RBfitResult method) (pyrosetta.rosetta.protocols.electron_density.RBfitResultComparitor method) (pyrosetta.rosetta.protocols.electron_density.RefinementResult method) (pyrosetta.rosetta.protocols.electron_density.RefinementResultComparitor method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator method) (pyrosetta.rosetta.protocols.electron_density.RevRefinementResultComparitor method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator method) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator method) (pyrosetta.rosetta.protocols.energy_based_clustering.EBC_ClusterType method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) (pyrosetta.rosetta.protocols.environment.AutoCutData method) (pyrosetta.rosetta.protocols.environment.AutoCutDataCreator method) (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength method) (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength.PrioSubtype method) (pyrosetta.rosetta.protocols.environment.claims.ControlStrength method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasElement method) (pyrosetta.rosetta.protocols.environment.claims.CutElement method) (pyrosetta.rosetta.protocols.environment.claims.DOFElement method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim method) (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.environment.claims.JumpElement method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator method) (pyrosetta.rosetta.protocols.environment.DofUnlock method) (pyrosetta.rosetta.protocols.environment.EnvClaimBroker method) (pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult method) (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.EnvMoverCreator method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.environment.ScriptCMCreator method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator method) (pyrosetta.rosetta.protocols.enzdes.CstAction method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedyCreator method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMoverCreator method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighterOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehaviorCreator method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMoverCreator method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator.CompareMode method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.EsmPerplexityTensorflowProtocol method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetricCreator method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.PCA method) (pyrosetta.rosetta.protocols.evaluation.PoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_long_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_Size method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_SSize method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_unsigned_long_t method) (pyrosetta.rosetta.protocols.evaluation.TimeEvaluator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCostFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinderFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserterFilterCreator method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMoverCreator method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutationCreator method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BatchFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.clique_saver method) (pyrosetta.rosetta.protocols.features.DatabaseFilter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBDefType method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.FragmentPair method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.MetricData method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) (pyrosetta.rosetta.protocols.features.ProtocolFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RamachandranHash method) (pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T method) (pyrosetta.rosetta.protocols.features.Report method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.ReportToDBCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegment method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.Segment method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures.Taskop_id_name_factory_ method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TopCountOfAllInputs method) (pyrosetta.rosetta.protocols.features.TopCountOfEachInput method) (pyrosetta.rosetta.protocols.features.TopPercentOfAllInputs method) (pyrosetta.rosetta.protocols.features.TopPercentOfEachInput method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDBCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.boolean_operations method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CalculatorFilterCreator method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilterCreator method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilterCreator method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilterCreator method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.FilterFactory method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetricCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilterCreator method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilterCreator method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilterCreator method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilterCreator method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilterCreator method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilterCreator method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDRCreator method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutationCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevelsCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.MatchResidues method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMoverCreator method) (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergyCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.ResiduePair method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.TripletID method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbIGFactory method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph.Subsitution method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph.Subsitution method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph.Subsitution method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph.Subsitution method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerOperationType method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerSpecificationType method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) (pyrosetta.rosetta.protocols.fold_from_loops.utils.NubSegment method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCstsCreator method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.LineObject method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelData method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.forge.remodel.Segment method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.Contact method) (pyrosetta.rosetta.protocols.frag_picker.ContactCounts method) (pyrosetta.rosetta.protocols.frag_picker.ContactType method) (pyrosetta.rosetta.protocols.frag_picker.CS2ndShift method) (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentComparatorBase method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.JCouplingIO method) (pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareByScoreCombination_t method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug.sentry method) (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AdaptiveScoreHistogram method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore 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.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms 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.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCost method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnTuple 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.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity 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.ProlinePhiScore 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.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity 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) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GenKICPerturberEffect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementsEqual method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.FitnessFunction method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Vec1Hash method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMoverCreator method) (pyrosetta.rosetta.protocols.hbnet.compare_by_x method) (pyrosetta.rosetta.protocols.hbnet.compare_hbond_residues method) (pyrosetta.rosetta.protocols.hbnet.compare_hbond_resnums method) (pyrosetta.rosetta.protocols.hbnet.compare_net_vec method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator method) (pyrosetta.rosetta.protocols.hbnet.DecoratedNetworkState method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator method) (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct method) (pyrosetta.rosetta.protocols.hbnet.HBondResStruct method) (pyrosetta.rosetta.protocols.hbnet.NetworkState method) (pyrosetta.rosetta.protocols.hbnet.NetworkStateScoreComparator method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) (pyrosetta.rosetta.protocols.helix_capper.HelixNCapperMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.AddSearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.hotspot_hashing.CartesianSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.ComposeSearchPatterns method) (pyrosetta.rosetta.protocols.hotspot_hashing.ConstPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStub method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.hotspot_hashing.LSMSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover.ExecutionMode method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover.StructureOutputMode method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe.ExecutionMode method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe.StructureOutputMode method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbeCreator method) (pyrosetta.rosetta.protocols.hotspot_hashing.PartitionedSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.RotationSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternExpansion method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternTransform method) (pyrosetta.rosetta.protocols.hotspot_hashing.SICPatternAtTransform method) (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator method) (pyrosetta.rosetta.protocols.hotspot_hashing.StubStatus method) (pyrosetta.rosetta.protocols.hotspot_hashing.SurfaceSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.TestPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.VectorPair method) (pyrosetta.rosetta.protocols.hybridization.AlignOption method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DDomainParse method) (pyrosetta.rosetta.protocols.hybridization.detailedControlsTagSetting method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) (pyrosetta.rosetta.protocols.hybridization.HybridizeFoldtreeDynamic method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocolCreator method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.sampleEnum method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.hybridization.TMalign method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_Real method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_Size method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_vector_Real method) (pyrosetta.rosetta.protocols.indexed_structure_store.BackboneStub method) (pyrosetta.rosetta.protocols.indexed_structure_store.BackboneStubVectorRMSDComparator method) (pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookup method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupResult method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilterCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.LookupMode method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.OverlapDeleteMode method) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry method) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry method) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry method) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry method) (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfile method) (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileConfig method) (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileResult method) (pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureEntry method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider method) (pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetric method) (pyrosetta.rosetta.protocols.inverse_folding.MIFSTProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor.CompletionMessage method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.CompareTags method) (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobDistributorFactory method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterFactory method) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobOutputterFactory method) (pyrosetta.rosetta.protocols.jd2.JobOutputterObserver method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobResult method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.MoverAndChunkLibraryJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputSource method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputter method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputter method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.compare_job_nodes method) (pyrosetta.rosetta.protocols.jd3.CompletedJobOutput method) (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.NodeManagerStorageMatrix method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.ResultElements method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) (pyrosetta.rosetta.protocols.jd3.deallocation.deallocation_msg_type method) (pyrosetta.rosetta.protocols.jd3.deallocation.DeallocationMessage method) (pyrosetta.rosetta.protocols.jd3.deallocation.InputPoseDeallocationMessage method) (pyrosetta.rosetta.protocols.jd3.deallocation.ResourceDeallocationMessage method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputSource method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InputSource method) (pyrosetta.rosetta.protocols.jd3.JGJobNode method) (pyrosetta.rosetta.protocols.jd3.JGResultNode method) (pyrosetta.rosetta.protocols.jd3.Job method) (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) (pyrosetta.rosetta.protocols.jd3.job_distributors.VanillaJobDistributor method) (pyrosetta.rosetta.protocols.jd3.job_results.PoseJobResult method) (pyrosetta.rosetta.protocols.jd3.job_summaries.EnergyJobSummary method) (pyrosetta.rosetta.protocols.jd3.job_summaries.StandardPoseJobSummary method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater method) (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.jd3.JobDistributor method) (pyrosetta.rosetta.protocols.jd3.JobDistributorFactory method) (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) (pyrosetta.rosetta.protocols.jd3.JobOutputIndex method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.JobResult method) (pyrosetta.rosetta.protocols.jd3.jobs.MoverJob method) (pyrosetta.rosetta.protocols.jd3.JobStatus method) (pyrosetta.rosetta.protocols.jd3.JobSummary method) (pyrosetta.rosetta.protocols.jd3.JobTracker method) (pyrosetta.rosetta.protocols.jd3.JQKey method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputter method) (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.output.ResultOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) (pyrosetta.rosetta.protocols.jumping.BaseDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.BasePairingLibrary method) (pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.jumping.cstType method) (pyrosetta.rosetta.protocols.jumping.DisulfPairing method) (pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.DisulfTemplate method) (pyrosetta.rosetta.protocols.jumping.dofType method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSample method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSelector.JumpWeightDef method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSetup.JumpDef method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.MembraneJump method) (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.PairingTemplate method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup.JumpDef method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMoverCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList.Iterator method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem.Memento method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) (pyrosetta.rosetta.protocols.kinematic_closure.IdealParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMoverCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) (pyrosetta.rosetta.protocols.kinmatch.BruteFunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.FunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.KinFunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.KRSQuery method) (pyrosetta.rosetta.protocols.kinmatch.KRSQueryType method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.AssemblyFactory method) (pyrosetta.rosetta.protocols.legacy_sewing.Basis method) (pyrosetta.rosetta.protocols.legacy_sewing.basis_pair_equal_to method) (pyrosetta.rosetta.protocols.legacy_sewing.basis_pair_hash method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.coord_equal_to method) (pyrosetta.rosetta.protocols.legacy_sewing.coord_hash method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.legacy_sewing.HashResult method) (pyrosetta.rosetta.protocols.legacy_sewing.HashValue method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragmentsCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.Model method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.move_type method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyAssemblyScoreFunction method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyAssemblyScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyBlosumScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyCalciumMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyClashScorer 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) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewAtom method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewResidue method) (pyrosetta.rosetta.protocols.legacy_sewing.SewSegment method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Distribution method) (pyrosetta.rosetta.protocols.ligand_docking.DistributionMap method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.atmInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ChiInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OptHMode method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PointScoreComparator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoComp method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoCompdH method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Ligand_info method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo.Type method) (pyrosetta.rosetta.protocols.ligand_docking.LigandArea method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) (pyrosetta.rosetta.protocols.ligand_docking.RotateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.Transform_info method) (pyrosetta.rosetta.protocols.ligand_docking.TransformCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info method) (pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator method) (pyrosetta.rosetta.protocols.ligand_evolution.Crossover method) (pyrosetta.rosetta.protocols.ligand_evolution.ElitistSelector method) (pyrosetta.rosetta.protocols.ligand_evolution.EvolutionManager method) (pyrosetta.rosetta.protocols.ligand_evolution.EvolutionOptions method) (pyrosetta.rosetta.protocols.ligand_evolution.FragmentLibrary method) (pyrosetta.rosetta.protocols.ligand_evolution.IdentityFactory method) (pyrosetta.rosetta.protocols.ligand_evolution.Individual method) (pyrosetta.rosetta.protocols.ligand_evolution.Mutator method) (pyrosetta.rosetta.protocols.ligand_evolution.OffspringFactory method) (pyrosetta.rosetta.protocols.ligand_evolution.Population method) (pyrosetta.rosetta.protocols.ligand_evolution.Reaction method) (pyrosetta.rosetta.protocols.ligand_evolution.Reagent method) (pyrosetta.rosetta.protocols.ligand_evolution.RouletteSelector method) (pyrosetta.rosetta.protocols.ligand_evolution.Scorer method) (pyrosetta.rosetta.protocols.ligand_evolution.Selector method) (pyrosetta.rosetta.protocols.ligand_evolution.TournamentSelector method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_grower.DensSkeleton method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator method) (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.loop_grower.ResTorsions method) (pyrosetta.rosetta.protocols.loop_grower.RMSComparator method) (pyrosetta.rosetta.protocols.loop_grower.SheetPositions method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSamplerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroidCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatomCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) (pyrosetta.rosetta.protocols.loophash.BBData method) (pyrosetta.rosetta.protocols.loophash.BBExtraData 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.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LeapIndex method) (pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex method) (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifierCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapperCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Master method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash.WU_Header method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilterCreator method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoopsCreator method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.JSONFormattedLoopsFileReader method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ChainDirection method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.Loop_lt method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCMCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopResult method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator 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.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.LoopConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopFromFileData method) (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoaderCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefinerCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileData method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) (pyrosetta.rosetta.protocols.loops.RationalLoopComparator method) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier method) (pyrosetta.rosetta.protocols.loops.SerializedLoop method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.magnesium.SampleGrid method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) (pyrosetta.rosetta.protocols.make_rot_lib.CentroidRotNum method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputterCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibPolymerType method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) (pyrosetta.rosetta.protocols.make_rot_lib.TorsionRange method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.Bool3DGrid method) (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) (pyrosetta.rosetta.protocols.match.BumpGrid method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) (pyrosetta.rosetta.protocols.match.downstream.us_secmatch_hit_compare method) (pyrosetta.rosetta.protocols.match.downstream_hit method) (pyrosetta.rosetta.protocols.match.Hit method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.match_dspos1 method) (pyrosetta.rosetta.protocols.match.match_lite_equals method) (pyrosetta.rosetta.protocols.match.match_lite_hasher method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.match.MatcherMoverCreator method) (pyrosetta.rosetta.protocols.match.MatcherOutputStats method) (pyrosetta.rosetta.protocols.match.MatcherTask method) (pyrosetta.rosetta.protocols.match.MatchOutputTracker method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.output.BestMatchesCollection method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter method) (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchFilter method) (pyrosetta.rosetta.protocols.match.output.MatchGrouper method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.OutputWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseInserter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.ProcessorFactory method) (pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher method) (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) (pyrosetta.rosetta.protocols.match.ProbeRadius method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.FullChiSampleSet method) (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.match.upstream.ScaffoldBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.match.upstream_hit method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.CartesianMDCreator method) (pyrosetta.rosetta.protocols.md.Constraint method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.md.MDscheduleData method) (pyrosetta.rosetta.protocols.md.Rattle method) (pyrosetta.rosetta.protocols.md.Thermostat method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanFieldFactory method) (pyrosetta.rosetta.protocols.mean_field.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelixCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAnglesCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.geometry.Embedding method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.scoring.ElectricfieldLipidlayer method) (pyrosetta.rosetta.protocols.membrane.scoring.ElectricfieldLipidlayerCreator method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator method) (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) (pyrosetta.rosetta.protocols.membrane.scoring.MEnvElectroAtomParams method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpanInfo method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSamplerCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.MatchGrafter method) (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincSiteFinder method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator method) (pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealerCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloResetCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTestCreator method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.TrialResult method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) (pyrosetta.rosetta.protocols.motifs.BuildPosition method) (pyrosetta.rosetta.protocols.motifs.IRCollection method) (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator method) (pyrosetta.rosetta.protocols.motifs.MotifHit method) (pyrosetta.rosetta.protocols.motifs.MotifLibrary method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.DsspMoverCreator method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.moves.FastLinearFunc method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IfMoverCreator method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.LinearFunc method) (pyrosetta.rosetta.protocols.moves.MCA method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloExceptionConverge method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverFactory method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.MoverStatistics method) (pyrosetta.rosetta.protocols.moves.MoverStatus method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.PoseCondition method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver.ObserverType method) (pyrosetta.rosetta.protocols.moves.RampingFunc method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RampingMoverCreator method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RandomMoverCreator method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SequenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.SimulatedTempering method) (pyrosetta.rosetta.protocols.moves.StatsType method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.SwitchMoverCreator method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.moves.X11Colors method) (pyrosetta.rosetta.protocols.mpi_refinement.Clusterer method) (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Emperor method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refinement method) (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) (pyrosetta.rosetta.protocols.mpi_refinement.Serial_Refine method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler.WU_Header method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric.DOF method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.JobResultID_hash method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.ParsedTagCache method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.SortByLowEnergy method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager method) (pyrosetta.rosetta.protocols.multistate_design.MetricCalculatorFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateAggregateFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.multistate_design.PartitionAggregateFunction method) (pyrosetta.rosetta.protocols.multistate_design.PosType method) (pyrosetta.rosetta.protocols.multistate_design.PosTypeCreator method) (pyrosetta.rosetta.protocols.multistate_design.SingleState method) (pyrosetta.rosetta.protocols.multistate_design.SingleStateEntityData method) (pyrosetta.rosetta.protocols.multistate_design.SingleStateFitnessFunction method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.network.UIObserver method) (pyrosetta.rosetta.protocols.network.UIObserver.ObserverType method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergyCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer method) (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergyCreator method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMoverCreator method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergyCreator method) (pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE method) (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.EliminationReason method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.EliminationReason method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.QualityClass method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.EliminationReason method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.QualityClass method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover 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.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.FoldResonance method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.MethylNameLibrary method) (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) (pyrosetta.rosetta.protocols.normalmode.ContactStruct method) (pyrosetta.rosetta.protocols.normalmode.NormalMode method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator method) (pyrosetta.rosetta.protocols.optimize_weights.AddStatus method) (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData.DDG_Bind_File_Index method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.IterativeOptEDriver method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifuncMPIMessages method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataFactory method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType method) (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData method) (pyrosetta.rosetta.protocols.optimize_weights.WeightRangeConstraint method) (pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.BasicSimAnnealerRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage method) (pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFunc method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.ExpExpression method) (pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker 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.MPIMultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) (pyrosetta.rosetta.protocols.pack_daemon.PowExpression method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet method) (pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator 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) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperationCreator method) (pyrosetta.rosetta.protocols.parser.BluePrint method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.parser.FragmentReader method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.FragSetLoaderCreator method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoaderCreator method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoader method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoaderCreator method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotentialCreator method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesCreator method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification method) (pyrosetta.rosetta.protocols.peptide_deriver.CyclizationMethod method) (pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo method) (pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverEntryType method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat method) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.Mutant method) (pyrosetta.rosetta.protocols.pmut_scan.MutationData method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.DarcParticleSwarmMinimizer method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid.PtType method) (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster.Cxyz method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.ray_distance_derivs method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) (pyrosetta.rosetta.protocols.pockets.spherical_coor_triplet method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pockets.triplet_and_originnum method) (pyrosetta.rosetta.protocols.pockets.UnionEdge method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.SSElement method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.BackboneStubRMSDComparator method) (pyrosetta.rosetta.protocols.pose_length_moves.Chain method) (pyrosetta.rosetta.protocols.pose_length_moves.chain_lt method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.FinalRMSDComparator method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) (pyrosetta.rosetta.protocols.pose_metric_calculators.CatPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ChargeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ClashCountCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.EmptyVertexData method) (pyrosetta.rosetta.protocols.pose_metric_calculators.EnergiesData method) (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.HPatchCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.MetricValueGetter method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NonlocalContactsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PackstatCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PiPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionByChainCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerRecovery method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SaltBridgeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SemiExplicitWaterUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SequenceComparison method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SurfaceCalculator method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.FilterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByPropertyCreator method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.DsspShiftArray method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorerCreator method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CSSettings method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilterCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SeedSettings method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.protein_grid.ProteinGrid method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.TorsionCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreakCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspotsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPoseCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.CoordinateConstraintStack method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbondsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinderCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChangeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLineCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodelCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspotCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransformCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoopCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutationCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimizeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.mutt method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.tm_region method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTreeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactorCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCstsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamersCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstructionType method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_interface_design.Transformation method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetricCreator method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocolBase method) (pyrosetta.rosetta.protocols.qsar.ColorGradient method) (pyrosetta.rosetta.protocols.qsar.qsarCreator method) (pyrosetta.rosetta.protocols.qsar.qsarMap method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.qsarOptData method) (pyrosetta.rosetta.protocols.qsar.qsarOptFunc method) (pyrosetta.rosetta.protocols.qsar.qsarPoint method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemageCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AllAtomNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChiAngleNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridManager method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HeavyAtomNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.MolecularWeightNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoreNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoaderCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetricCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.RB_lt method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.Histogram method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.recces.params.RECCES_Parameters method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizerCreator method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMoverCreator method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMoverCreator method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMoverCreator method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelaxCreator method) (pyrosetta.rosetta.protocols.relax.DatabaseRelaxScript method) (pyrosetta.rosetta.protocols.relax.EnergyMapContainer method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.FastRelaxCreator method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelaxCreator method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RelaxScriptCommand method) (pyrosetta.rosetta.protocols.relax.RelaxScriptFileContents method) (pyrosetta.rosetta.protocols.relax.RelaxScriptManager method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelaxCreator method) (pyrosetta.rosetta.protocols.relax.VariableSubstitutionPair method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax.WU_Header method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore.WU_Header method) (pyrosetta.rosetta.protocols.residue_optimization.MetapatchEnumeration method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelectorCreator method) (pyrosetta.rosetta.protocols.rigid.Direction method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.Partner method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RollMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCMCreator method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMoverCreator method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergyCreator method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.SourcePositions method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMoverCreator method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.FilterReportTime method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocolCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFlags method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsSchemaValidator method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) (pyrosetta.rosetta.protocols.rotamer_gen.FragmentRotamers method) (pyrosetta.rosetta.protocols.rotamer_gen.FragmentRotamersCreator method) (pyrosetta.rosetta.protocols.rotamer_gen.RDKitRotamers method) (pyrosetta.rosetta.protocols.rotamer_gen.RDKitRotamersCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.OutputLevel method) (pyrosetta.rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSDCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiffCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiffCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBins method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBinsCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPack method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPackCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamers method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamersCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructureCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelaxCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrials method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrialsCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMinCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHumanCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimple method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimpleCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLiteCreator method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.rpc.BasicCmdLineInit method) (pyrosetta.rosetta.protocols.rpc.BasicInit method) (pyrosetta.rosetta.protocols.rpc.JSON_RPC method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilterCreator method) (pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.GridSearchIterator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PseudocontactShiftEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManagerSingleton method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor 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.GridSearchIterator_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PseudocontactShiftEnergyCreator_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.TensorsOptimizer_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.TensorsOptimizer_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.GridSearchIterator_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PseudocontactShiftEnergyCreator_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.TensorsOptimizer_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.GridSearchIterator_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_manager_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PseudocontactShiftEnergyCreator_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.TensorsOptimizer_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegmentsCreator method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGeneratorCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFoldCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCstCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoopsCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptidesCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptidesSegment method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTreeCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMoverCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizerCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentSpec method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegmentCreator method) (pyrosetta.rosetta.protocols.sewing.data_storage.Basis method) (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandContact method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.PolymericType method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFGMSettings method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMoverCreator method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentSettings method) (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.coord_equal_to method) (pyrosetta.rosetta.protocols.sewing.hashing.coord_hash method) (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) (pyrosetta.rosetta.protocols.sewing.hashing.HasherSettings method) (pyrosetta.rosetta.protocols.sewing.hashing.HashValue method) (pyrosetta.rosetta.protocols.sewing.hashing.IdealContact method) (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) (pyrosetta.rosetta.protocols.sewing.hashing.LigandCoordInfo method) (pyrosetta.rosetta.protocols.sewing.hashing.ModelFileReader method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementFactory method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandAssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerFactory method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorerCreator method) (pyrosetta.rosetta.protocols.sic_dock.AtomIDHashFunction method) (pyrosetta.rosetta.protocols.sic_dock.BuriedPolarScore method) (pyrosetta.rosetta.protocols.sic_dock.CBScore method) (pyrosetta.rosetta.protocols.sic_dock.ConstraintSetScore method) (pyrosetta.rosetta.protocols.sic_dock.EdgeStandScore method) (pyrosetta.rosetta.protocols.sic_dock.HelixScore method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.sic_dock.LinkerScore method) (pyrosetta.rosetta.protocols.sic_dock.RigidScore method) (pyrosetta.rosetta.protocols.sic_dock.Rose method) (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) (pyrosetta.rosetta.protocols.sic_dock.scores.TrisBpyScore method) (pyrosetta.rosetta.protocols.sic_dock.SICFast method) (pyrosetta.rosetta.protocols.sic_dock.Vec3 method) (pyrosetta.rosetta.protocols.sic_dock.XfoxmScore method) (pyrosetta.rosetta.protocols.sic_dock.xyzStripeHashPoseWithMeta method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScanFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.ddGCreator method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScanCreator method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVectorFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BatchEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BatchNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BSAF_mode method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreakFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.comparison_type method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExternalEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LoopRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseCommentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.Quat method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFrag method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.mutt method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.tm_region method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SelectGdtEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectMaxsubEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinderFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinderFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.StructuralSimilarityEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TruncatedScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilterCreator method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AtomHash method) (pyrosetta.rosetta.protocols.simple_moves.AtomHashNode method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.chiral.Chirality method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideCyclizationViability method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator method) (pyrosetta.rosetta.protocols.simple_moves.FragmentCost method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GunnCost method) (pyrosetta.rosetta.protocols.simple_moves.GunnTuple method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover.Item method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionPerturbType method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.TumbleCreator method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.WaterRot method) (pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.BuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack1 method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack2 method) (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterfaceCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsCreator method) (pyrosetta.rosetta.protocols.sparta.ANN method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluator method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.sparta.GDB method) (pyrosetta.rosetta.protocols.sparta.PDB method) (pyrosetta.rosetta.protocols.sparta.PDB_Entry method) (pyrosetta.rosetta.protocols.sparta.RingData method) (pyrosetta.rosetta.protocols.sparta.Sparta method) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator method) (pyrosetta.rosetta.protocols.splice.BBDofs method) (pyrosetta.rosetta.protocols.splice.BBMatching method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBInMoverCreator method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RBOutMoverCreator method) (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) (pyrosetta.rosetta.protocols.splice.ROT method) (pyrosetta.rosetta.protocols.splice.RotLibdb method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.RotLibOutCreator method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceCreator method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceInTailCreator method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.SpliceOutTailCreator method) (pyrosetta.rosetta.protocols.splice.SpliceSegment method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.splice.TailSegmentMoverCreator method) (pyrosetta.rosetta.protocols.ss_prediction.SS_predictor method) (pyrosetta.rosetta.protocols.star.Extender method) (pyrosetta.rosetta.protocols.star.StarAbinitio method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) (pyrosetta.rosetta.protocols.stepwise.modeler.MinimizerMode method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker.ProteinAtrRepChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.InternalWorkingResidueParameter method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body.BaseBin method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body.compare_base_bin method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body.compare_int_pair method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.TransientCutpointHandler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.submotif.SubMotifLibrary method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeSet method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.screener.RNA_TorsionScreener method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceParameters method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoaderCreator method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.boolean_operations method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinCore method) (pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.STMStoredTask method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator method) (pyrosetta.rosetta.protocols.tcr.TCRloopRefine method) (pyrosetta.rosetta.protocols.tcr.TCRmodel method) (pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts method) (pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo method) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi method) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterOptions method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DummyClass method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.IGInterfaceEdgeUpweighter method) (pyrosetta.rosetta.protocols.toolbox.IGLigandDesignEdgeUpweighter method) (pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleConstraint method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.Node method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.Base method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_1A method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_1B method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2A method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2A2B method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2B method) (pyrosetta.rosetta.protocols.toolbox.ResidueGroupIGEdgeUpweighter method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.protocols.toolbox.SF_Replica method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage method) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim.ClaimRight method) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim.ClaimRight method) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim.ClaimRight method) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim.ClaimRight method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim.ClaimRight method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim.ClaimRight method) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim.ClaimRight method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer 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.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) (pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.ConstAbinitioMoverWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.LargeFragWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.SmallFragWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.SmoothFragWeight method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryReader method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter.Frame method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaOutputs_v1 method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaOutputsBase method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaProtocol_v1 method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaProtocolBase method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneMinimizationMode method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneRandomizationMode method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMoverCreator method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) (pyrosetta.rosetta.protocols.viewer.graphics_states_param.BBdisplayState method) (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode method) (pyrosetta.rosetta.protocols.viewer.graphics_states_param.SCdisplayState method) (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ShowHState method) (pyrosetta.rosetta.protocols.viewer.graphics_states_param.TrajectoryState method) (pyrosetta.rosetta.protocols.viewer.GraphicsState method) (pyrosetta.rosetta.protocols.viewer.SilentObserver method) (pyrosetta.rosetta.protocols.viewer.spheremode method) (pyrosetta.rosetta.protocols.viewer.triangle method) (pyrosetta.rosetta.protocols.viewer.triangleIterator method) (pyrosetta.rosetta.protocols.vip.VIP_Mover method) (pyrosetta.rosetta.protocols.vip.VIP_Report method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit.WU_Header method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.protocols.wum.MoverList method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager_Slave method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper.WU_Header method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore.WU_Header method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait.WU_Header method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase.WU_Header method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnitManager method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) (pyrosetta.rosetta.protocols.wum.WUM_MPI_TAGS method) (pyrosetta.rosetta.RDGeom.Point method) (pyrosetta.rosetta.RDGeom.Point3D method) (pyrosetta.rosetta.RDGeom.Transform3D method) (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.BondIterator_ method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.RDKit.Dict method) (pyrosetta.rosetta.RDKit.Dict.Pair method) (pyrosetta.rosetta.RDKit.RDProps method) (pyrosetta.rosetta.RDKit.RDValue method) (pyrosetta.rosetta.RDKit.RingInfo method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) (pyrosetta.rosetta.RDNumeric.Matrix_double_t method) (pyrosetta.rosetta.RDNumeric.SquareMatrix_double_t method) (pyrosetta.rosetta.RDNumeric.Vector_double_t method) (pyrosetta.rosetta.RNAAtomType method) (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) (pyrosetta.rosetta.std.binary_function_basic_datacache_ResRotPair_basic_datacache_ResRotPair_bool_t method) (pyrosetta.rosetta.std.binary_function_std_pair_char_char_std_pair_char_char_bool_t method) (pyrosetta.rosetta.std.binary_function_unsigned_long_unsigned_long_bool_t method) (pyrosetta.rosetta.std.equal_to_basic_datacache_ResRotPair_t method) (pyrosetta.rosetta.std.equal_to_std_pair_char_char_t method) (pyrosetta.rosetta.std.equal_to_unsigned_long_t method) (pyrosetta.rosetta.std.error_code method) (pyrosetta.rosetta.std.error_condition method) (pyrosetta.rosetta.std.exception method) (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.fpos___mbstate_t_t method) (pyrosetta.rosetta.std.hash_unsigned_long_t method) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.ifstream.sentry method) (pyrosetta.rosetta.std.integral_constant_bool_false_t method) (pyrosetta.rosetta.std.integral_constant_bool_true_t method) (pyrosetta.rosetta.std.ios_base method) (pyrosetta.rosetta.std.ios_base.event method) (pyrosetta.rosetta.std.ios_base.failure method) (pyrosetta.rosetta.std.ios_base.Init method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.iostream.sentry method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istream.sentry method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.istringstream.sentry method) (pyrosetta.rosetta.std.ItemsView method) (pyrosetta.rosetta.std.KeysView method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.std.locale method) (pyrosetta.rosetta.std.locale._Impl method) (pyrosetta.rosetta.std.locale.id method) (pyrosetta.rosetta.std.map_char_double method) (pyrosetta.rosetta.std.map_char_protocols_pose_sewing_movers_SeedSettings method) (pyrosetta.rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_char_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.map_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t_std_allocator_std_pair_const_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t method) (pyrosetta.rosetta.std.map_char_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_char_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_char_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_core_chemical_AA_double method) (pyrosetta.rosetta.std.map_core_chemical_AA_std_pair_double_double_t_std_allocator_std_pair_const_core_chemical_AA_std_pair_double_double_t method) (pyrosetta.rosetta.std.map_core_chemical_AA_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_core_environment_LocalPosition_double method) (pyrosetta.rosetta.std.map_core_id_AtomID_bool method) (pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID method) (pyrosetta.rosetta.std.map_core_id_AtomID_double method) (pyrosetta.rosetta.std.map_core_id_AtomID_unsigned_long method) (pyrosetta.rosetta.std.map_core_id_AtomID_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_core_id_AtomID_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_core_scoring_rmsd_atoms_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_core_scoring_rmsd_atoms_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_core_scoring_ScoreType_double method) (pyrosetta.rosetta.std.map_int_int method) (pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model method) (pyrosetta.rosetta.std.map_int_utility_vector0_float_std_allocator_float_t_std_allocator_std_pair_const_int_utility_vector0_float_std_allocator_float_t method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_protocols_loops_Loop method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_core_chemical_AA_std_allocator_core_chemical_AA_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_core_chemical_AA_std_allocator_core_chemical_AA_t method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBPose_std_allocator_protocols_antibody_CDRDBPose_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBPose_std_allocator_protocols_antibody_CDRDBPose_t method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBSequence_std_allocator_protocols_antibody_CDRDBSequence_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBSequence_std_allocator_protocols_antibody_CDRDBSequence_t method) (pyrosetta.rosetta.std.map_protocols_antibody_clusters_CDRClusterEnum_utility_vector1_protocols_antibody_design_MutantPosition_std_allocator_protocols_antibody_design_MutantPosition_t_std_allocator_std_pair_const_protocols_antibody_clusters_CDRClusterEnum_utility_vector1_protocols_antibody_design_MutantPosition_std_allocator_protocols_antibody_design_MutantPosition_t method) (pyrosetta.rosetta.std.map_protocols_carbohydrates_GlycanSequon_std_string method) (pyrosetta.rosetta.std.map_std_pair_core_chemical_AA_core_chemical_AA_t_double_std_less_std_pair_core_chemical_AA_core_chemical_AA_t_std_allocator_std_pair_const_std_pair_core_chemical_AA_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_std_pair_core_id_AtomID_core_id_AtomID_t_utility_vector1_double_std_allocator_double_t_std_less_std_pair_core_id_AtomID_core_id_AtomID_t_std_allocator_std_pair_const_std_pair_core_id_AtomID_core_id_AtomID_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t method) (pyrosetta.rosetta.std.map_std_pair_std_string_std_string_t_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t_std_less_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_pair_std_string_std_string_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_std_string_t_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_less_std_pair_unsigned_long_std_string_t_std_allocator_std_pair_const_std_pair_unsigned_long_std_string_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_unsigned_long_t_std_set_protocols_sewing_hashing_LigandCoordInfo_t_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_std_set_protocols_sewing_hashing_LigandCoordInfo_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_unsigned_long_t_unsigned_long_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_unsigned_long_std_less_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_std_allocator_std_pair_const_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_string_bool method) (pyrosetta.rosetta.std.map_std_string_char method) (pyrosetta.rosetta.std.map_std_string_core_chemical_AA method) (pyrosetta.rosetta.std.map_std_string_core_chemical_carbohydrates_RootData method) (pyrosetta.rosetta.std.map_std_string_core_chemical_carbohydrates_SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.std.map_std_string_core_conformation_symmetry_VirtualCoordinate method) (pyrosetta.rosetta.std.map_std_string_core_id_NamedAtomID method) (pyrosetta.rosetta.std.map_std_string_core_io_CisPeptideInformation method) (pyrosetta.rosetta.std.map_std_string_core_io_ModifiedResidueInformation method) (pyrosetta.rosetta.std.map_std_string_core_io_nmr_ParaIon method) (pyrosetta.rosetta.std.map_std_string_core_io_nmr_SpinlabelDatabaseEntry method) (pyrosetta.rosetta.std.map_std_string_core_io_pdb_RecordType method) (pyrosetta.rosetta.std.map_std_string_core_pose_Pose method) (pyrosetta.rosetta.std.map_std_string_core_scoring_rmsd_atoms method) (pyrosetta.rosetta.std.map_std_string_double method) (pyrosetta.rosetta.std.map_std_string_float method) (pyrosetta.rosetta.std.map_std_string_int method) (pyrosetta.rosetta.std.map_std_string_numeric_interpolation_spline_LinearFunction method) (pyrosetta.rosetta.std.map_std_string_numeric_xyzVector_double_t_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.map_std_string_protocols_denovo_design_components_Alias method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcs2_PcsInputFile method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcs_PCS_file_data method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs1_PCS_file_data_Ts1 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs2_PCS_file_data_Ts2 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs3_PCS_file_data_Ts3 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs4_PCS_file_data_Ts4 method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t_std_allocator_std_pair_const_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t_std_allocator_std_pair_const_std_string_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_pair_core_chemical_io_merge_residue_behavior_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_core_chemical_io_merge_residue_behavior_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_pair_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_utility_vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_std_allocator_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_utility_vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_std_allocator_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_set_std_shared_ptr_basic_datacache_WriteableCacheableData_t_std_allocator_std_pair_const_std_string_std_set_std_shared_ptr_basic_datacache_WriteableCacheableData_t method) (pyrosetta.rosetta.std.map_std_string_std_set_std_string_t_std_allocator_std_pair_const_std_string_std_set_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_MetricValueBase_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_MetricValueBase_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_resource_manager_ResourceLoaderCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_resource_manager_ResourceLoaderCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_resource_manager_ResourceLocatorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_resource_manager_ResourceLocatorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_core_chemical_Metapatch_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_core_chemical_Metapatch_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_utility_tag_Tag_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_palette_PackerPaletteCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_palette_PackerPaletteCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_operation_TaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_TaskOperationCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_ResfileCommand_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pose_Pose_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_scoring_motif_MotifHash_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_scoring_motif_MotifHash_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_numeric_expression_parser_VariableExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_numeric_expression_parser_VariableExpression_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_FilterCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_filters_FilterCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_moves_MoverCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_moves_MoverCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_parser_DataLoaderCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_parser_DataLoaderCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t method) (pyrosetta.rosetta.std.map_std_string_std_string method) (pyrosetta.rosetta.std.map_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_std_string_t_std_allocator_std_pair_const_std_string_std_vector_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_string_unsigned_long method) (pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t_std_allocator_std_pair_const_std_string_utility_vector1_char_std_allocator_char_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t_std_allocator_std_pair_const_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t_std_allocator_std_pair_const_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.std.map_unsigned_long_bool method) (pyrosetta.rosetta.std.map_unsigned_long_char method) (pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof method) (pyrosetta.rosetta.std.map_unsigned_long_double method) (pyrosetta.rosetta.std.map_unsigned_long_numeric_xyzVector_double_t_std_allocator_std_pair_const_unsigned_long_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_dna_DnaNeighbor method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_dna_DnaPosition method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_indexed_structure_store_FragmentLookupResult method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_sewing_hashing_IdealContact method) (pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_pair_char_std_string_t_std_allocator_std_pair_const_unsigned_long_std_pair_char_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_pair_double_double_t_std_allocator_std_pair_const_unsigned_long_std_pair_double_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_t_std_allocator_std_pair_const_unsigned_long_std_set_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_protocols_sewing_data_storage_LigandResidue_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_protocols_sewing_data_storage_LigandResidue_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_fragment_FragSet_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_io_PositionDdGInfo_PositionDdGInfo_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_io_PositionDdGInfo_PositionDdGInfo_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_scoring_epr_deer_metrics_DEERData_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_scoring_epr_deer_metrics_DEERData_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_LigandResidue_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_LigandResidue_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_string method) (pyrosetta.rosetta.std.map_unsigned_long_unsigned_long method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) 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(pyrosetta.rosetta.utility.io.GeneralFileManager method) (pyrosetta.rosetta.utility.io.GeneralFileManagerVector method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t.sentry method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostreambase_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS method) 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(pyrosetta.rosetta.utility.json_spirit.internal_.Type_to_type_long_t method) (pyrosetta.rosetta.utility.json_spirit.internal_.Type_to_type_unsigned_long_t method) (pyrosetta.rosetta.utility.json_spirit.Null method) (pyrosetta.rosetta.utility.json_spirit.Pair_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_type method) (pyrosetta.rosetta.utility.keys.AutoKey_utility_options_Option_utility_keys_Key_utility_keys_NoClient_t method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.Key2Tuple_double_double_t method) (pyrosetta.rosetta.utility.keys.Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.keys.Key3Tuple_protocols_loops_Loop_std_shared_ptr_core_kinematics_MoveMap_std_shared_ptr_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.keys.Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.keys.Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.keys.KeyLookup_utility_options_OptionKey_t method) (pyrosetta.rosetta.utility.keys.NoClient method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) (pyrosetta.rosetta.utility.keys.VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.utility.LexicographicalIterator method) (pyrosetta.rosetta.utility.libsvm.Svm_node_rosetta method) (pyrosetta.rosetta.utility.libsvm.Svm_rosetta method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.OptionTypes method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey 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.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey 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.options.VectorOptionKey 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) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.OverloadTest method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.Show method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.LinkUnit method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.SimpleRange1 method) (pyrosetta.rosetta.utility.simulate_mpi_message_type method) (pyrosetta.rosetta.utility.SimulateMPI method) (pyrosetta.rosetta.utility.SimulateMPIData method) (pyrosetta.rosetta.utility.SimulateMPIMessage method) (pyrosetta.rosetta.utility.SingletonBase_basic_citation_manager_CitationManager_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_datacache_WriteableCacheableDataFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_mpi_MessageListenerFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_resource_manager_ResourceLoaderFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_resource_manager_ResourceLocatorFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_resource_manager_ResourceManagerFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_sampling_orientations_QuaternionGridManager_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_tensorflow_manager_RosettaTensorflowManager_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_thread_manager_RosettaThreadManager_t method) (pyrosetta.rosetta.utility.SingletonBase_basic_thread_manager_RosettaThreadManagerInitializationTracker_t method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_AtomPropertiesManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_carbohydrates_CarbohydrateInfoManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_ChemicalManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_orbitals_OrbitalTypeMapper_t method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_PatchOperationFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_rings_RingConformerManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_chemical_rotamers_RotamerLibrarySpecificationFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_energy_methods_GridInfo_t method) (pyrosetta.rosetta.utility.SingletonBase_core_energy_methods_WaterWeightGridSet_t method) (pyrosetta.rosetta.utility.SingletonBase_core_enzymes_EnzymeManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_fragment_picking_old_FragmentLibraryManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_import_pose_libraries_RNA_LibraryManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_io_nmr_ParamagneticDatabaseHandler_t method) (pyrosetta.rosetta.utility.SingletonBase_core_io_nmr_SpinlabelDatabaseHandler_t method) (pyrosetta.rosetta.utility.SingletonBase_core_io_NomenclatureManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_io_pdb_RecordCollection_t method) (pyrosetta.rosetta.utility.SingletonBase_core_io_silent_SilentStructFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_dunbrack_cenrot_CenrotLibrary_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_dunbrack_RotamerLibrary_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_guidance_scoreterms_sap_SapDatabase_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_interaction_graph_RotamerDotsRadiusData_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_interaction_graph_SurfacePotential_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_palette_PackerPaletteFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_rotamers_SingleResidueRotamerLibraryFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_task_operation_ResFilterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_task_operation_ResLvlTaskOperationFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_pack_task_operation_TaskOperationFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_bin_transitions_BinTransitionCalculatorManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_constraints_ConstraintFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_constraints_ConstraintIO_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_lkball_LKBallDatabase_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_motif_MotifHashManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_nmr_NMRDataFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_saxs_SinXOverX_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_ScoreFunctionFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_scoring_ScoringManager_t method) (pyrosetta.rosetta.utility.SingletonBase_core_select_jump_selector_JumpSelectorFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_select_residue_selector_ResidueSelectorFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_sequence_SequenceFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_core_simple_metrics_SimpleMetricFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_numeric_model_quality_RmsData_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_antibody_grafting_RegExManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_antibody_grafting_SCS_Helper_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_chemistries_ChemistryFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_constraint_generator_ConstraintGeneratorFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_constraint_generator_ConstraintsManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_constraint_generator_HydrogenBondInfo_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_architects_DeNovoArchitectFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_components_Picker_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_components_StructureDataFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_task_operations_ConsensusLoopDatabase_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_docking_DockingHighResFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_drug_design_bcl_BCLReferenceSDFilesManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_drug_design_bcl_BCLSampleConfsManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_drug_design_SAScoreData_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_evaluation_EvaluatorFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_features_FeaturesReporterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_filters_FilterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_genetic_algorithm_EntityElementFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_indexed_structure_store_FragmentStoreManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_indexed_structure_store_StructureStoreManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd2_JobInputterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd2_JobOutputterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd3_full_model_inputters_FullModelInputterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd3_pose_inputters_PoseInputterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jd3_pose_outputters_PoseOutputterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jumping_StandardDisulfPairingLibrary_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_jumping_StandardPairingLibrary_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_legacy_sewing_sampling_requirements_LegacyRequirementFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_ligand_docking_DistributionMap_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_ligand_docking_rdf_RDFFunctionFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_loops_loop_mover_refine_LoopRefineInnerCycleFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_loops_LoopMoverFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_loops_loops_definers_LoopsDefinerFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_matdes_SymDofMoverSampler_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_moves_MoverFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_multistage_rosetta_scripts_cluster_ClusterMetricFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_noesy_assign_CovalentCompliance_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_noesy_assign_MethylNameLibrary_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_parser_DataLoaderFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_qsar_scoring_grid_GridFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_qsar_scoring_grid_GridManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_relax_RelaxScriptManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_rosetta_scripts_PosePropertyReporterFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_rosetta_scripts_PoseSelectorFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_rosetta_scripts_RosettaScriptsSchemaValidator_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_rotamer_recovery_RotamerRecoveryFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_InterchainPotential_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs2_PcsDataCenterManagerSingleton_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs2_PcsEnergyParameterManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs2_PcsGridSearchParameterManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs2_PcsInputCenterManager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs_PCS_data_input_manager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcs_PCS_Energy_parameters_manager_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcsTs1_PCS_Energy_parameters_manager_Ts1_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcsTs2_PCS_Energy_parameters_manager_Ts2_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcsTs3_PCS_Energy_parameters_manager_Ts3_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_methods_pcsTs4_PCS_Energy_parameters_manager_Ts4_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_sewing_requirements_AssemblyRequirementFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_sewing_scoring_AssemblyScorerFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_protocols_topology_broker_TopologyClaimerFactory_t method) (pyrosetta.rosetta.utility.SingletonBase_utility_Inline_File_Provider_t method) (pyrosetta.rosetta.utility.SingletonBase_utility_io_GeneralFileManager_t method) (pyrosetta.rosetta.utility.SingletonBase_utility_io_GeneralFileManagerVector_t method) (pyrosetta.rosetta.utility.SingletonBase_utility_sql_database_DatabaseSessionManager_t method) (pyrosetta.rosetta.utility.sql_database.DatabaseMode method) (pyrosetta.rosetta.utility.sql_database.DatabaseMode.e method) (pyrosetta.rosetta.utility.sql_database.DatabaseSessionManager method) (pyrosetta.rosetta.utility.sql_database.session method) (pyrosetta.rosetta.utility.sql_database.transaction method) (pyrosetta.rosetta.utility.sql_database.TransactionMode method) (pyrosetta.rosetta.utility.sql_database.TransactionMode.e method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_MResIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_NodeIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_RotamerIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_NStructIndex_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_PrelimJobNodeID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_ResultIndex_t method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.AutoBool method) (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior method) (pyrosetta.rosetta.utility.tag.Tag method) (pyrosetta.rosetta.utility.tag.XMLErrorHandler method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaCommonType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaDataType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaElementCategory method) (pyrosetta.rosetta.utility.tag.XMLSchemaMinOccursMaxOccurs method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroupType method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestrictionType method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary.ElementType method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.tag.XMLValidationOutput method) (pyrosetta.rosetta.utility.tag.XMLValidator method) (pyrosetta.rosetta.utility.thread.MutableCache_const_core_chemical_ResidueTypeSet__star__core_pack_palette_BaseTypeList_t method) (pyrosetta.rosetta.utility.type_traits.has_insertion_operator_implementation.any_type method) (pyrosetta.rosetta.utility.type_traits.has_insertion_operator_implementation.False method) (pyrosetta.rosetta.utility.type_traits.is_string_constructible_char__star__t method) (pyrosetta.rosetta.utility.type_traits.is_string_constructible_const_char__star__t method) (pyrosetta.rosetta.utility.type_traits.is_string_constructible_const_std_string__ref__t method) (pyrosetta.rosetta.utility.type_traits.is_string_constructible_const_std_string_t method) (pyrosetta.rosetta.utility.type_traits.is_string_constructible_const_utility_tag_XMLSchemaType__ref__t method) (pyrosetta.rosetta.utility.type_traits.is_string_constructible_std_string__ref__t method) (pyrosetta.rosetta.utility.type_traits.is_string_constructible_std_string_t method) (pyrosetta.rosetta.utility.type_traits.is_string_constructible_utility_tag_XMLSchemaType_t method) (pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin method) (pyrosetta.rosetta.utility.vector0_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector0_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector0_double method) (pyrosetta.rosetta.utility.vector0_float method) (pyrosetta.rosetta.utility.vector0_int method) (pyrosetta.rosetta.utility.vector0_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.utility.vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector0_std_pair_float_float_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.utility.vector0_std_string method) (pyrosetta.rosetta.utility.vector0_unsigned_char method) (pyrosetta.rosetta.utility.vector0_unsigned_long method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_lkball_WaterBuilder method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_drug_design_ReactionBasedAnalogSampler_Reagent method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_evolution_Individual method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_std_less_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_std_pair_const_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_DOF_ID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_NamedAtomID_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_raw_data_DisulfideFile_ResNum_core_io_raw_data_DisulfideFile_ResNum_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_aa_composition_energy_TailFunction_core_scoring_aa_composition_energy_TailFunction_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_CentroidDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_DisulfideMatchingEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_FullatomDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_std_shared_ptr_const_core_conformation_ResidueMatcher_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_long_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_float_int_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_forge_build_Interval_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_loophash_BackboneSegment_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_sewing_data_storage_Basis_protocols_sewing_data_storage_Basis_t method) 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(pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_calc_taskop_movers_DesignRepackMover_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_calc_taskop_movers_DesignRepackMover_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_filters_Filter_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_genetic_algorithm_Entity_std_pair_utility_vector1_double_std_allocator_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_unsigned_long_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_std_allocator_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_std_allocator_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) (pyrosetta.rosetta.utility.vectorL_IndexSelector_false_t method) (pyrosetta.rosetta.utility.vectorL_IndexSelector_true_t method) (pyrosetta.rosetta.utility.vectorL_ZeroSelector_false_t method) (pyrosetta.rosetta.utility.vectorL_ZeroSelector_true_t method) (pyrosetta.rosetta.utility.Version method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType method) (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType method) (pyrosetta.rosetta.utility_exit_detail.Stringifier method) (pyrosetta.rosetta.utility_exit_detail.Stringy method) _read_file() (pyrosetta.rosetta.core.io.silent.SilentFileData method) _reisude_pair_energies() (in module pyrosetta.toolbox.atom_pair_energy) _replace() (pyrosetta.CD method) _repr_pretty_() (pyrosetta.bindings.pose.PoseResidueLabelAccessor method) (pyrosetta.bindings.pose.PoseScoreAccessor method) (pyrosetta.bindings.pose.ResidueLabelAccessor method) _reserved (pyrosetta.bindings.pose.PoseScoreAccessor attribute) _RESULTS (class in pyrosetta.rosetta.core.scoring.sc) _RNA_MatchType_ (class in pyrosetta.rosetta.core.fragment.rna) _rosetta_database_from_env() (in module pyrosetta) _rotation_axis_angle_instantiation_for_PyRosetta() (in module pyrosetta.rosetta.numeric) _static_type_name() (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD static method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD static method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD static method) (pyrosetta.rosetta.core.fragment.Frame static method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD static method) (pyrosetta.rosetta.core.fragment.JumpingFrame static method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame static method) (pyrosetta.rosetta.core.fragment.SecstructSRFD static method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData static method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion static method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController static method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController static method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 static method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 static method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 static method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 static method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer static method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer static method) _stored_derivatives (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization property) (pyrosetta.rosetta.core.optimization.BrentLineMinimization property) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm property) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization property) _truncateMessage() (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) _vector_extend_func() (in module pyrosetta) _version_string() (in module pyrosetta) _VOID (pyrosetta.rosetta.protocols.enzdes.CstAction attribute) _write_silent_struct() (pyrosetta.rosetta.core.io.silent.SilentFileData method) _xmlNode (class in pyrosetta.rosetta) _xx (pyrosetta.rosetta.core.optimization.BrentLineMinimization property)