Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | W | Z A add_codec() (gufe.custom_json.JSONSerializerDeserializer method) AlchemicalNetwork (class in gufe.network) allowed_nonbonded() (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) annotations (gufe.mapping.ligandatommapping.LigandAtomMapping property) arbitrary_types_allowed (gufe.settings.models.Settings.Config attribute) (gufe.settings.models.SettingsBaseModel.Config attribute) (gufe.settings.models.ThermoSettings.Config attribute) args (gufe.storage.errors.ChangedExternalResourceError attribute) (gufe.storage.errors.ExternalResourceError attribute) (gufe.storage.errors.MissingExternalResourceError attribute) AtomMapper (class in gufe.mapping.atom_mapper) AtomMapping (class in gufe.mapping.atom_mapping) B BaseForceFieldSettings (class in gufe.settings.models) BaseForceFieldSettings.Config (class in gufe.settings.models) BLUE (in module gufe.visualization.mapping_visualization) C capitalize() (gufe.tokenization.GufeKey method) casefold() (gufe.tokenization.GufeKey method) center() (gufe.tokenization.GufeKey method) ChangedExternalResourceError ChemicalSystem (class in gufe.chemicalsystem) Component (class in gufe.components.component) component_diff() (gufe.chemicalsystem.ChemicalSystem method) componentA (gufe.mapping.atom_mapping.AtomMapping property) (gufe.mapping.ligandatommapping.LigandAtomMapping property) componentA_to_componentB (gufe.mapping.atom_mapping.AtomMapping property) (gufe.mapping.ligandatommapping.LigandAtomMapping property) componentA_unique (gufe.mapping.atom_mapping.AtomMapping property) (gufe.mapping.ligandatommapping.LigandAtomMapping property) componentB (gufe.mapping.atom_mapping.AtomMapping property) (gufe.mapping.ligandatommapping.LigandAtomMapping property) componentB_to_componentA (gufe.mapping.atom_mapping.AtomMapping property) (gufe.mapping.ligandatommapping.LigandAtomMapping property) componentB_unique (gufe.mapping.atom_mapping.AtomMapping property) (gufe.mapping.ligandatommapping.LigandAtomMapping property) ComponentMapping (class in gufe.mapping.componentmapping) components (gufe.chemicalsystem.ChemicalSystem property) connected_subgraphs() (gufe.network.AlchemicalNetwork method) constraint_check() (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) constraints (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) Context (class in gufe.protocols.protocolunit) copy_with_replacements() (gufe.components.smallmoleculecomponent.SmallMoleculeComponent method) (gufe.tokenization.GufeTokenizable method) count() (gufe.tokenization.GufeKey method) create() (gufe.protocols.protocol.Protocol method) (gufe.transformations.transformation.NonTransformation method) (gufe.transformations.transformation.Transformation method) (gufe.transformations.transformation.TransformationBase method) custom_json_factory() (in module gufe.custom_json) D DAGMixin (class in gufe.protocols.protocoldag) data (gufe.protocols.protocol.ProtocolResult property) decoder (gufe.custom_json.JSONSerializerDeserializer attribute) default() (gufe.custom_json.JSONCodec method) default_from_dict() (in module gufe.custom_codecs) default_settings() (gufe.protocols.protocol.Protocol class method) defaults() (gufe.tokenization.GufeTokenizable class method) delete() (gufe.storage.externalresource.base.ExternalStorage method) (gufe.storage.externalresource.filestorage.FileStorage method) (gufe.storage.externalresource.memorystorage.MemoryStorage method) dependencies (gufe.protocols.protocolunit.ProtocolUnit property) (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) deserialize_numpy() (in module gufe.molhashing) deserializer() (gufe.custom_json.JSONSerializerDeserializer method) dict_decode_dependencies() (in module gufe.tokenization) dict_encode_dependencies() (in module gufe.tokenization) draw_mapping() (in module gufe.visualization.mapping_visualization) draw_one_molecule_mapping() (in module gufe.visualization.mapping_visualization) draw_to_file() (gufe.mapping.ligandatommapping.LigandAtomMapping method) draw_unhighlighted_molecule() (in module gufe.visualization.mapping_visualization) dump() (gufe.transformations.transformation.NonTransformation method) (gufe.transformations.transformation.Transformation method) (gufe.transformations.transformation.TransformationBase method) E edges (gufe.ligandnetwork.LigandNetwork property) (gufe.network.AlchemicalNetwork property) encode() (gufe.tokenization.GufeKey method) encoder (gufe.custom_json.JSONSerializerDeserializer attribute) end_time (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) endswith() (gufe.tokenization.GufeKey method) enlarge_graph() (gufe.ligandnetwork.LigandNetwork method) ensure_filelike (class in gufe.utils) exception (gufe.protocols.protocolunit.ProtocolUnitFailure property) execute() (gufe.protocols.protocolunit.ProtocolUnit method) execute_DAG() (in module gufe.protocols.protocoldag) exists() (gufe.storage.externalresource.base.ExternalStorage method) (gufe.storage.externalresource.filestorage.FileStorage method) (gufe.storage.externalresource.memorystorage.MemoryStorage method) expandtabs() (gufe.tokenization.GufeKey method) ExplicitMoleculeComponent (class in gufe.components.explicitmoleculecomponent) extends_key (gufe.protocols.protocoldag.DAGMixin property) ExternalResourceError ExternalStorage (class in gufe.storage.externalresource.base) extra (gufe.settings.models.Settings.Config attribute) (gufe.settings.models.SettingsBaseModel.Config attribute) (gufe.settings.models.ThermoSettings.Config attribute) F FileStorage (class in gufe.storage.externalresource.filestorage) find() (gufe.tokenization.GufeKey method) forcefield_settings (gufe.settings.models.Settings attribute) forcefields (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) format() (gufe.tokenization.GufeKey method) format_map() (gufe.tokenization.GufeKey method) from_dict() (gufe.tokenization.GufeTokenizable class method) (in module gufe.tokenization) from_graphml() (gufe.ligandnetwork.LigandNetwork class method) (gufe.network.AlchemicalNetwork class method) from_gufe() (gufe.tokenization.KeyedChain class method) from_json() (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent class method) (gufe.components.proteincomponent.ProteinComponent class method) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent class method) (gufe.tokenization.GufeTokenizable class method) from_keyed_chain() (gufe.tokenization.GufeTokenizable class method) from_keyed_chain_rep() (gufe.tokenization.KeyedChain class method) from_keyed_dict() (gufe.tokenization.GufeTokenizable class method) from_openff() (gufe.components.smallmoleculecomponent.SmallMoleculeComponent class method) from_pdb_file() (gufe.components.proteincomponent.ProteinComponent class method) from_pdbx_file() (gufe.components.proteincomponent.ProteinComponent class method) from_rdkit() (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent class method) (gufe.components.proteincomponent.ProteinComponent class method) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent class method) from_sdf_file() (gufe.components.smallmoleculecomponent.SmallMoleculeComponent class method) from_sdf_string() (gufe.components.smallmoleculecomponent.SmallMoleculeComponent class method) from_shallow_dict() (gufe.tokenization.GufeTokenizable class method) frozen_copy() (gufe.settings.models.BaseForceFieldSettings method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings method) (gufe.settings.models.Settings method) (gufe.settings.models.SettingsBaseModel method) (gufe.settings.models.ThermoSettings method) G gather() (gufe.protocols.protocol.Protocol method) (gufe.transformations.transformation.NonTransformation method) (gufe.transformations.transformation.Transformation method) (gufe.transformations.transformation.TransformationBase method) get_all_gufe_objs() (in module gufe.tokenization) get_class() (in module gufe.tokenization) get_defaults() (gufe.settings.models.Settings class method) get_distances() (gufe.mapping.ligandatommapping.LigandAtomMapping method) get_estimate() (gufe.protocols.protocol.ProtocolResult method) get_filename() (gufe.storage.externalresource.base.ExternalStorage method) (gufe.storage.externalresource.filestorage.FileStorage method) (gufe.storage.externalresource.memorystorage.MemoryStorage method) get_metadata() (gufe.storage.externalresource.base.ExternalStorage method) (gufe.storage.externalresource.filestorage.FileStorage method) (gufe.storage.externalresource.memorystorage.MemoryStorage method) get_uncertainty() (gufe.protocols.protocol.ProtocolResult method) graph (gufe.ligandnetwork.LigandNetwork property) (gufe.network.AlchemicalNetwork property) (gufe.protocols.protocoldag.DAGMixin property) (gufe.protocols.protocoldag.ProtocolDAG attribute) gufe.chemicalsystem module gufe.components module gufe.components.component module gufe.components.explicitmoleculecomponent module gufe.components.proteincomponent module gufe.components.smallmoleculecomponent module gufe.components.solventcomponent module gufe.custom_codecs module gufe.custom_json module gufe.custom_typing module gufe.ligandnetwork module gufe.mapping module gufe.mapping.atom_mapper module gufe.mapping.atom_mapping module gufe.mapping.componentmapping module gufe.mapping.ligandatommapping module gufe.molhashing module gufe.network module gufe.protocols module gufe.protocols.protocol module gufe.protocols.protocoldag module gufe.protocols.protocolunit module gufe.settings module gufe.settings.models module gufe.storage module gufe.storage.errors module gufe.storage.externalresource module gufe.storage.externalresource.base module gufe.storage.externalresource.filestorage module gufe.storage.externalresource.memorystorage module gufe.tokenization module gufe.transformations module gufe.transformations.transformation module gufe.utils module gufe.visualization module gufe.visualization.mapping_visualization module gufe_keys() (gufe.tokenization.KeyedChain method) gufe_objects_from_shallow_dict() (in module gufe.tokenization) gufe_to_digraph() (in module gufe.tokenization) gufe_to_keyed_chain_rep() (gufe.tokenization.KeyedChain static method) GufeKey (class in gufe.tokenization) GufeTokenizable (class in gufe.tokenization) H hydrogen_mass (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) I import_qualname() (in module gufe.tokenization) index() (gufe.tokenization.GufeKey method) inherited_is_my_dict() (in module gufe.custom_codecs) inputs (gufe.protocols.protocolunit.ProtocolUnit property) (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) ion_concentration (gufe.components.solventcomponent.SolventComponent property) is_connected() (gufe.ligandnetwork.LigandNetwork method) is_frozen (gufe.settings.models.BaseForceFieldSettings property) (gufe.settings.models.OpenMMSystemGeneratorFFSettings property) (gufe.settings.models.Settings property) (gufe.settings.models.SettingsBaseModel property) (gufe.settings.models.ThermoSettings property) is_gufe_dict() (in module gufe.tokenization) is_gufe_key_dict() (in module gufe.tokenization) is_gufe_obj() (in module gufe.tokenization) is_npy_dtype_dict() (in module gufe.custom_codecs) is_openff_quantity_dict() (in module gufe.custom_codecs) is_openff_unit_dict() (in module gufe.custom_codecs) is_positive_distance() (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) isalnum() (gufe.tokenization.GufeKey method) isalpha() (gufe.tokenization.GufeKey method) isascii() (gufe.tokenization.GufeKey method) isdecimal() (gufe.tokenization.GufeKey method) isdigit() (gufe.tokenization.GufeKey method) isidentifier() (gufe.tokenization.GufeKey method) islower() (gufe.tokenization.GufeKey method) isnumeric() (gufe.tokenization.GufeKey method) isprintable() (gufe.tokenization.GufeKey method) isspace() (gufe.tokenization.GufeKey method) istitle() (gufe.tokenization.GufeKey method) isupper() (gufe.tokenization.GufeKey method) iter_contents() (gufe.storage.externalresource.base.ExternalStorage method) (gufe.storage.externalresource.filestorage.FileStorage method) (gufe.storage.externalresource.memorystorage.MemoryStorage method) J join() (gufe.tokenization.GufeKey method) JSONCodec (class in gufe.custom_json) JSONSerializerDeserializer (class in gufe.custom_json) K key (gufe.tokenization.GufeTokenizable property) key_decode_dependencies() (in module gufe.tokenization) key_encode_dependencies() (in module gufe.tokenization) key_renamed() (in module gufe.tokenization) keyed_dicts() (gufe.tokenization.KeyedChain method) KeyedChain (class in gufe.tokenization) L LigandAtomMapping (class in gufe.mapping.ligandatommapping) LigandNetwork (class in gufe.ligandnetwork) ljust() (gufe.tokenization.GufeKey method) load() (gufe.transformations.transformation.NonTransformation class method) (gufe.transformations.transformation.Transformation class method) (gufe.transformations.transformation.TransformationBase class method) load_stream() (gufe.storage.externalresource.base.ExternalStorage method) (gufe.storage.externalresource.filestorage.FileStorage method) (gufe.storage.externalresource.memorystorage.MemoryStorage method) logger (gufe.tokenization.GufeTokenizable property) lower() (gufe.tokenization.GufeKey method) lstrip() (gufe.tokenization.GufeKey method) M maketrans() (gufe.tokenization.GufeKey static method) mapping (gufe.transformations.transformation.Transformation property) md5 (gufe.storage.externalresource.base.Metadata attribute) MemoryStorage (class in gufe.storage.externalresource.memorystorage) Metadata (class in gufe.storage.externalresource.base) MissingExternalResourceError modify_dependencies() (in module gufe.tokenization) module gufe.chemicalsystem gufe.components gufe.components.component gufe.components.explicitmoleculecomponent gufe.components.proteincomponent gufe.components.smallmoleculecomponent gufe.components.solventcomponent gufe.custom_codecs gufe.custom_json gufe.custom_typing gufe.ligandnetwork gufe.mapping gufe.mapping.atom_mapper gufe.mapping.atom_mapping gufe.mapping.componentmapping gufe.mapping.ligandatommapping gufe.molhashing gufe.network gufe.protocols gufe.protocols.protocol gufe.protocols.protocoldag gufe.protocols.protocolunit gufe.settings gufe.settings.models gufe.storage gufe.storage.errors gufe.storage.externalresource gufe.storage.externalresource.base gufe.storage.externalresource.filestorage gufe.storage.externalresource.memorystorage gufe.tokenization gufe.transformations gufe.transformations.transformation gufe.utils gufe.visualization gufe.visualization.mapping_visualization module_qualname() (in module gufe.tokenization) N n_protocol_dag_results (gufe.protocols.protocol.ProtocolResult property) name (gufe.chemicalsystem.ChemicalSystem property) (gufe.components.component.Component property) (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent property) (gufe.components.proteincomponent.ProteinComponent property) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent property) (gufe.components.solventcomponent.SolventComponent property) (gufe.network.AlchemicalNetwork property) (gufe.protocols.protocoldag.DAGMixin property) (gufe.protocols.protocoldag.ProtocolDAG attribute) (gufe.protocols.protocolunit.ProtocolUnit property) (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) (gufe.transformations.transformation.NonTransformation property) (gufe.transformations.transformation.Transformation property) (gufe.transformations.transformation.TransformationBase property) negative_ion (gufe.components.solventcomponent.SolventComponent property) negative_ions (in module gufe.components.proteincomponent) nested_key_moved() (in module gufe.tokenization) neutralize (gufe.components.solventcomponent.SolventComponent property) new_key_added() (in module gufe.tokenization) nodes (gufe.ligandnetwork.LigandNetwork property) (gufe.network.AlchemicalNetwork property) nonbonded_cutoff (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) nonbonded_method (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) NonTransformation (class in gufe.transformations.transformation) O object_hook() (gufe.custom_json.JSONCodec method) ok() (gufe.protocols.protocoldag.ProtocolDAGResult method) (gufe.protocols.protocolunit.ProtocolUnitFailure static method) (gufe.protocols.protocolunit.ProtocolUnitResult static method) old_key_removed() (in module gufe.tokenization) OpenMMSystemGeneratorFFSettings (class in gufe.settings.models) OpenMMSystemGeneratorFFSettings.Config (class in gufe.settings.models) outputs (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) P partition() (gufe.tokenization.GufeKey method) ph (gufe.settings.models.ThermoSettings attribute) positive_ion (gufe.components.solventcomponent.SolventComponent property) positive_ions (in module gufe.components.proteincomponent) prefix (gufe.tokenization.GufeKey property) pressure (gufe.settings.models.ThermoSettings attribute) ProteinComponent (class in gufe.components.proteincomponent) Protocol (class in gufe.protocols.protocol) protocol (gufe.transformations.transformation.NonTransformation property) (gufe.transformations.transformation.Transformation property) (gufe.transformations.transformation.TransformationBase property) protocol_unit_failures (gufe.protocols.protocoldag.ProtocolDAGResult property) protocol_unit_results (gufe.protocols.protocoldag.ProtocolDAGResult property) protocol_unit_successes (gufe.protocols.protocoldag.ProtocolDAGResult property) protocol_units (gufe.protocols.protocoldag.DAGMixin property) (gufe.protocols.protocoldag.ProtocolDAG attribute) ProtocolDAG (class in gufe.protocols.protocoldag) ProtocolDAGResult (class in gufe.protocols.protocoldag) ProtocolResult (class in gufe.protocols.protocol) ProtocolUnit (class in gufe.protocols.protocolunit) ProtocolUnitFailure (class in gufe.protocols.protocolunit) ProtocolUnitResult (class in gufe.protocols.protocolunit) R RED (in module gufe.visualization.mapping_visualization) redox_potential (gufe.settings.models.ThermoSettings attribute) register_tokenizable_class() (in module gufe.tokenization) REMAPPED_CLASSES (in module gufe.tokenization) removeprefix() (gufe.tokenization.GufeKey method) removesuffix() (gufe.tokenization.GufeKey method) replace() (gufe.tokenization.GufeKey method) result_cls (gufe.protocols.protocol.Protocol attribute) result_graph (gufe.protocols.protocoldag.ProtocolDAGResult property) result_to_unit() (gufe.protocols.protocoldag.ProtocolDAGResult method) rfind() (gufe.tokenization.GufeKey method) rigid_water (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) rindex() (gufe.tokenization.GufeKey method) rjust() (gufe.tokenization.GufeKey method) rpartition() (gufe.tokenization.GufeKey method) rsplit() (gufe.tokenization.GufeKey method) rstrip() (gufe.tokenization.GufeKey method) S scratch (gufe.protocols.protocolunit.Context attribute) serialization_migration() (gufe.tokenization.GufeTokenizable class method) serialize_numpy() (in module gufe.molhashing) serializer() (gufe.custom_json.JSONSerializerDeserializer method) Settings (class in gufe.settings.models) settings (gufe.protocols.protocol.Protocol property) Settings.Config (class in gufe.settings.models) SettingsBaseModel (class in gufe.settings.models) SettingsBaseModel.Config (class in gufe.settings.models) shared (gufe.protocols.protocolunit.Context attribute) small_molecule_forcefield (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) SmallMoleculeComponent (class in gufe.components.smallmoleculecomponent) smart_union (gufe.settings.models.Settings.Config attribute) (gufe.settings.models.SettingsBaseModel.Config attribute) (gufe.settings.models.ThermoSettings.Config attribute) smiles (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent property) (gufe.components.proteincomponent.ProteinComponent property) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent property) (gufe.components.solventcomponent.SolventComponent property) SolventComponent (class in gufe.components.solventcomponent) source_key (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) split() (gufe.tokenization.GufeKey method) splitlines() (gufe.tokenization.GufeKey method) start_time (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) startswith() (gufe.tokenization.GufeKey method) stateA (gufe.transformations.transformation.NonTransformation property) (gufe.transformations.transformation.Transformation property) (gufe.transformations.transformation.TransformationBase property) stateB (gufe.transformations.transformation.NonTransformation property) (gufe.transformations.transformation.Transformation property) (gufe.transformations.transformation.TransformationBase property) store_bytes() (gufe.storage.externalresource.base.ExternalStorage method) (gufe.storage.externalresource.filestorage.FileStorage method) (gufe.storage.externalresource.memorystorage.MemoryStorage method) store_path() (gufe.storage.externalresource.base.ExternalStorage method) (gufe.storage.externalresource.filestorage.FileStorage method) (gufe.storage.externalresource.memorystorage.MemoryStorage method) strip() (gufe.tokenization.GufeKey method) suggest_mappings() (gufe.mapping.atom_mapper.AtomMapper method) swapcase() (gufe.tokenization.GufeKey method) system (gufe.transformations.transformation.NonTransformation property) T temperature (gufe.settings.models.ThermoSettings attribute) terminal_protocol_unit_results (gufe.protocols.protocoldag.ProtocolDAGResult property) thermo_settings (gufe.settings.models.Settings attribute) ThermoSettings (class in gufe.settings.models) ThermoSettings.Config (class in gufe.settings.models) title() (gufe.tokenization.GufeKey method) to_dict() (gufe.storage.externalresource.base.Metadata method) (gufe.tokenization.GufeKey method) (gufe.tokenization.GufeTokenizable method) (in module gufe.tokenization) to_graphml() (gufe.ligandnetwork.LigandNetwork method) (gufe.network.AlchemicalNetwork method) to_gufe() (gufe.tokenization.KeyedChain method) to_json() (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent method) (gufe.components.proteincomponent.ProteinComponent method) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent method) (gufe.tokenization.GufeTokenizable method) to_keyed_chain() (gufe.tokenization.GufeTokenizable method) to_keyed_chain_rep() (gufe.tokenization.KeyedChain method) to_keyed_dict() (gufe.tokenization.GufeTokenizable method) to_openff() (gufe.components.smallmoleculecomponent.SmallMoleculeComponent method) to_openmm_positions() (gufe.components.proteincomponent.ProteinComponent method) to_openmm_topology() (gufe.components.proteincomponent.ProteinComponent method) to_pdb_file() (gufe.components.proteincomponent.ProteinComponent method) to_pdbx_file() (gufe.components.proteincomponent.ProteinComponent method) to_rbfe_alchemical_network() (gufe.ligandnetwork.LigandNetwork method) to_rdkit() (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent method) (gufe.components.proteincomponent.ProteinComponent method) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent method) to_sdf() (gufe.components.smallmoleculecomponent.SmallMoleculeComponent method) to_shallow_dict() (gufe.tokenization.GufeTokenizable method) token (gufe.tokenization.GufeKey property) TOKENIZABLE_CLASS_REGISTRY (in module gufe.tokenization) TOKENIZABLE_REGISTRY (in module gufe.tokenization) tokenize() (in module gufe.tokenization) total_charge (gufe.chemicalsystem.ChemicalSystem property) (gufe.components.component.Component property) (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent property) (gufe.components.proteincomponent.ProteinComponent property) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent property) (gufe.components.solventcomponent.SolventComponent property) traceback (gufe.protocols.protocolunit.ProtocolUnitFailure property) Transformation (class in gufe.transformations.transformation) transformation_key (gufe.protocols.protocoldag.DAGMixin property) TransformationBase (class in gufe.transformations.transformation) translate() (gufe.tokenization.GufeKey method) U unfrozen_copy() (gufe.settings.models.BaseForceFieldSettings method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings method) (gufe.settings.models.Settings method) (gufe.settings.models.SettingsBaseModel method) (gufe.settings.models.ThermoSettings method) unit_to_all_results() (gufe.protocols.protocoldag.ProtocolDAGResult method) unit_to_result() (gufe.protocols.protocoldag.ProtocolDAGResult method) upper() (gufe.tokenization.GufeKey method) W with_annotations() (gufe.mapping.ligandatommapping.LigandAtomMapping method) with_traceback() (gufe.storage.errors.ChangedExternalResourceError method) (gufe.storage.errors.ExternalResourceError method) (gufe.storage.errors.MissingExternalResourceError method) Z zfill() (gufe.tokenization.GufeKey method)