Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Z A add_codec() (gufe.serialization.json.JSONSerializerDeserializer method) add_note() (gufe.components.errors.ComponentValidationError method) (gufe.mapping.errors.AtomMappingError method) (gufe.protocols.errors.ExecutionInterrupt method) (gufe.protocols.errors.GufeProtocolError method) (gufe.protocols.errors.MissingUnitResultError method) (gufe.protocols.errors.ProtocolDAGError method) (gufe.protocols.errors.ProtocolDAGExecutionError method) (gufe.protocols.errors.ProtocolDAGResultError method) (gufe.protocols.errors.ProtocolUnitExecutionError method) (gufe.protocols.errors.ProtocolUnitFailureError method) (gufe.protocols.errors.ProtocolValidationError method) (gufe.storage.errors.ChangedExternalResourceError method) (gufe.storage.errors.ExternalResourceError method) (gufe.storage.errors.MissingExternalResourceError method) AlchemicalArchive (class in gufe.archival) AlchemicalNetwork (class in gufe.network) allowed_nonbonded_methods() (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) AngstromQuantity (in module gufe.settings.typing) annotations (gufe.mapping.ligandatommapping.LigandAtomMapping property) args (gufe.components.errors.ComponentValidationError attribute) (gufe.mapping.errors.AtomMappingError attribute) (gufe.protocols.errors.ExecutionInterrupt attribute) (gufe.protocols.errors.GufeProtocolError attribute) (gufe.protocols.errors.MissingUnitResultError attribute) (gufe.protocols.errors.ProtocolDAGError attribute) (gufe.protocols.errors.ProtocolDAGExecutionError attribute) (gufe.protocols.errors.ProtocolDAGResultError attribute) (gufe.protocols.errors.ProtocolUnitExecutionError attribute) (gufe.protocols.errors.ProtocolUnitFailureError attribute) (gufe.protocols.errors.ProtocolValidationError attribute) (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) AtomMappingError B BarQuantity (in module gufe.settings.typing) BaseForceFieldSettings (class in gufe.settings.models) BaseSolventComponent (class in gufe.components.solventcomponent) BoxQuantity (in module gufe.settings.typing) 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.componentmapping.ComponentMapping 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.componentmapping.ComponentMapping 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) ComponentValidationError connected_subgraphs() (gufe.network.AlchemicalNetwork method) constraints (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) construct() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) contains() (gufe.chemicalsystem.ChemicalSystem method) Context (class in gufe.protocols.protocolunit) 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) 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.serialization.json) D DAGMixin (class in gufe.protocols.protocoldag) data (gufe.protocols.protocol.ProtocolResult property) DATETIME (gufe.serialization.msgpack.MPEXT attribute) decode_subchains() (gufe.tokenization.KeyedChain method) decoder (gufe.serialization.json.JSONSerializerDeserializer attribute) default() (gufe.serialization.json.JSONCodec method) default_from_dict() (in module gufe.serialization.json) 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) density (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent property) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent property) dependencies (gufe.protocols.protocolunit.ProtocolUnit property) (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) deserialize_numpy() (in module gufe.molhashing) deserializer() (gufe.serialization.json.JSONSerializerDeserializer method) dict() (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) dict_decode_dependencies() (in module gufe.tokenization) dict_encode_dependencies() (in module gufe.tokenization) display_mapping_3d() (in module gufe.visualization.mapping_visualization) display_mappings_3d() (in module gufe.visualization.mapping_visualization) 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.serialization.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) ExecutionInterrupt 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) ext_hook_default() (in module gufe.serialization.msgpack) extends_key (gufe.protocols.protocoldag.DAGMixin property) (gufe.protocols.protocoldag.ProtocolDAG property) (gufe.protocols.protocoldag.ProtocolDAGResult property) ExternalResourceError ExternalStorage (class in gufe.storage.externalresource.base) 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.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_msgpack() (gufe.tokenization.GufeTokenizable class method) from_openff() (gufe.components.smallmoleculecomponent.SmallMoleculeComponent class method) from_orm() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) from_pdb_file() (gufe.components.proteincomponent.ProteinComponent class method) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent class method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent class method) from_pdbx_file() (gufe.components.proteincomponent.ProteinComponent class method) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent class method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent class method) from_rdkit() (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent class method) (gufe.components.proteincomponent.ProteinComponent class method) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent class method) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent class method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent 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() (gufe.chemicalsystem.ChemicalSystem method) get_alchemical_charge_difference() (gufe.mapping.ligandatommapping.LigandAtomMapping method) get_all_gufe_objs() (in module gufe.tokenization) get_class() (in module gufe.tokenization) get_components_of_type() (gufe.chemicalsystem.ChemicalSystem method) 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 property) (gufe.protocols.protocoldag.ProtocolDAGResult property) gufe.archival module gufe.chemicalsystem module gufe.components module gufe.components.component module gufe.components.errors module gufe.components.explicitmoleculecomponent module gufe.components.proteincomponent module gufe.components.smallmoleculecomponent module gufe.components.solvatedpdbcomponent module gufe.components.solventcomponent 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.errors module gufe.mapping.ligandatommapping module gufe.molhashing module gufe.network module gufe.protocols module gufe.protocols.errors module gufe.protocols.protocol module gufe.protocols.protocoldag module gufe.protocols.protocolunit module gufe.serialization module gufe.serialization.json module gufe.serialization.msgpack module gufe.settings module gufe.settings.models module gufe.settings.typing 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) GufeArrayQuantity (in module gufe.settings.typing) GufeKey (class in gufe.tokenization) GufeProtocolError GufeQuantity (in module gufe.settings.typing) 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.serialization.json) 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.serialization.json) is_openff_quantity_dict() (in module gufe.serialization.json) is_openff_unit_dict() (in module gufe.serialization.json) is_python_313_path_dict() (in module gufe.serialization.json) 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) items() (gufe.chemicalsystem.ChemicalSystem 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) json() (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) JSONCodec (class in gufe.serialization.json) JSONSerializerDeserializer (class in gufe.serialization.json) K KCalPerMolQuantity (in module gufe.settings.typing) KelvinQuantity (in module gufe.settings.typing) 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) keys() (gufe.chemicalsystem.ChemicalSystem method) L LARGEINT (gufe.serialization.msgpack.MPEXT attribute) 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 magic_open() (in module gufe.utils) 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) metadata (gufe.archival.AlchemicalArchive property) (gufe.transformations.transformation.NonTransformation property) (gufe.transformations.transformation.Transformation property) (gufe.transformations.transformation.TransformationBase property) MissingExternalResourceError MissingUnitResultError model_computed_fields (gufe.settings.models.BaseForceFieldSettings attribute) (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) (gufe.settings.models.Settings attribute) (gufe.settings.models.SettingsBaseModel attribute) (gufe.settings.models.ThermoSettings attribute) model_config (gufe.settings.models.BaseForceFieldSettings attribute) (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) (gufe.settings.models.Settings attribute) (gufe.settings.models.SettingsBaseModel attribute) (gufe.settings.models.ThermoSettings attribute) model_construct() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) model_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) model_dump() (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) model_dump_json() (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) model_extra (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) model_fields (gufe.settings.models.BaseForceFieldSettings attribute) (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) (gufe.settings.models.Settings attribute) (gufe.settings.models.SettingsBaseModel attribute) (gufe.settings.models.ThermoSettings attribute) model_fields_set (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) model_json_schema() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) model_parametrized_name() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) model_post_init() (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) model_rebuild() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) model_validate() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) model_validate_json() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) model_validate_strings() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) modify_dependencies() (in module gufe.tokenization) module gufe.archival gufe.chemicalsystem gufe.components gufe.components.component gufe.components.errors gufe.components.explicitmoleculecomponent gufe.components.proteincomponent gufe.components.smallmoleculecomponent gufe.components.solvatedpdbcomponent gufe.components.solventcomponent gufe.custom_typing gufe.ligandnetwork gufe.mapping gufe.mapping.atom_mapper gufe.mapping.atom_mapping gufe.mapping.componentmapping gufe.mapping.errors gufe.mapping.ligandatommapping gufe.molhashing gufe.network gufe.protocols gufe.protocols.errors gufe.protocols.protocol gufe.protocols.protocoldag gufe.protocols.protocolunit gufe.serialization gufe.serialization.json gufe.serialization.msgpack gufe.settings gufe.settings.models gufe.settings.typing 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) MPEXT (class in gufe.serialization.msgpack) N n_protocol_dag_results (gufe.protocols.protocol.ProtocolResult property) n_waters (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent 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.solvatedpdbcomponent.ProteinMembraneComponent property) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent property) (gufe.components.solventcomponent.BaseSolventComponent property) (gufe.components.solventcomponent.SolventComponent property) (gufe.network.AlchemicalNetwork property) (gufe.protocols.protocoldag.DAGMixin property) (gufe.protocols.protocoldag.ProtocolDAG property) (gufe.protocols.protocoldag.ProtocolDAGResult property) (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) NanometerArrayQuantity (in module gufe.settings.typing) NanometerQuantity (in module gufe.settings.typing) NanosecondQuantity (in module gufe.settings.typing) NDARRAY (gufe.serialization.msgpack.MPEXT attribute) negative_ion (gufe.components.solventcomponent.SolventComponent property) nested_key_moved() (in module gufe.tokenization) network (gufe.archival.AlchemicalArchive property) 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) NPGENERIC (gufe.serialization.msgpack.MPEXT attribute) O object_hook() (gufe.serialization.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) outputs (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) P pack_default() (in module gufe.serialization.msgpack) pack_largeint() (in module gufe.serialization.msgpack) packb() (in module gufe.serialization.msgpack) parse_file() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) parse_obj() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) parse_raw() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) partition() (gufe.tokenization.GufeKey method) PATH (gufe.serialization.msgpack.MPEXT attribute) ph (gufe.settings.models.ThermoSettings attribute) PicosecondQuantity (in module gufe.settings.typing) positive_ion (gufe.components.solventcomponent.SolventComponent property) prefix (gufe.tokenization.GufeKey property) pressure (gufe.settings.models.ThermoSettings attribute) ProteinComponent (class in gufe.components.proteincomponent) ProteinMembraneComponent (class in gufe.components.solvatedpdbcomponent) 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 property) (gufe.protocols.protocoldag.ProtocolDAGResult property) ProtocolDAG (class in gufe.protocols.protocoldag) ProtocolDAGError ProtocolDAGExecutionError ProtocolDAGResult (class in gufe.protocols.protocoldag) ProtocolDAGResultError ProtocolResult (class in gufe.protocols.protocol) ProtocolUnit (class in gufe.protocols.protocolunit) ProtocolUnitExecutionError ProtocolUnitFailure (class in gufe.protocols.protocolunit) ProtocolUnitFailureError ProtocolUnitResult (class in gufe.protocols.protocolunit) ProtocolValidationError R 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) requires_package() (in module gufe.utils) 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 schema() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) schema_json() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) scratch (gufe.protocols.protocolunit.Context attribute) serialization_migration() (gufe.tokenization.GufeTokenizable class method) serialize_numpy() (in module gufe.molhashing) serializer() (gufe.serialization.json.JSONSerializerDeserializer method) Settings (class in gufe.settings.models) settings (gufe.protocols.protocol.Protocol property) SETTINGS (gufe.serialization.msgpack.MPEXT attribute) SettingsBaseModel (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) smiles (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent property) (gufe.components.proteincomponent.ProteinComponent property) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent property) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent property) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent property) (gufe.components.solventcomponent.SolventComponent property) SolvatedPDBComponent (class in gufe.components.solvatedpdbcomponent) SolventComponent (class in gufe.components.solventcomponent) source_key (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) specify_quantity_units() (in module gufe.settings.typing) 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) stderr (gufe.protocols.protocolunit.Context attribute) (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult property) stdout (gufe.protocols.protocolunit.Context attribute) (gufe.protocols.protocolunit.ProtocolUnitFailure property) (gufe.protocols.protocolunit.ProtocolUnitResult 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) 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.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_msgpack() (gufe.tokenization.GufeTokenizable method) to_openff() (gufe.components.smallmoleculecomponent.SmallMoleculeComponent method) to_openmm_positions() (gufe.components.proteincomponent.ProteinComponent method) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent method) to_openmm_topology() (gufe.components.proteincomponent.ProteinComponent method) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent method) to_pdb_file() (gufe.components.proteincomponent.ProteinComponent method) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent method) to_pdbx_file() (gufe.components.proteincomponent.ProteinComponent method) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent 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) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent 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.solvatedpdbcomponent.ProteinMembraneComponent property) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent property) (gufe.components.solventcomponent.BaseSolventComponent 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) (gufe.protocols.protocoldag.ProtocolDAG property) (gufe.protocols.protocoldag.ProtocolDAGResult property) transformation_results (gufe.archival.AlchemicalArchive property) TransformationBase (class in gufe.transformations.transformation) translate() (gufe.tokenization.GufeKey method) trim_graph() (gufe.ligandnetwork.LigandNetwork 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 (gufe.serialization.msgpack.MPEXT attribute) unit_to_all_results() (gufe.protocols.protocoldag.ProtocolDAGResult method) unit_to_result() (gufe.protocols.protocoldag.ProtocolDAGResult method) unpackb() (in module gufe.serialization.msgpack) update_forward_refs() (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) upper() (gufe.tokenization.GufeKey method) UUID (gufe.serialization.msgpack.MPEXT attribute) V validate() (gufe.components.component.Component method) (gufe.components.explicitmoleculecomponent.ExplicitMoleculeComponent method) (gufe.components.proteincomponent.ProteinComponent method) (gufe.components.smallmoleculecomponent.SmallMoleculeComponent method) (gufe.components.solvatedpdbcomponent.ProteinMembraneComponent method) (gufe.components.solvatedpdbcomponent.SolvatedPDBComponent method) (gufe.components.solventcomponent.BaseSolventComponent method) (gufe.components.solventcomponent.SolventComponent method) (gufe.protocols.protocol.Protocol method) (gufe.settings.models.BaseForceFieldSettings class method) (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) (gufe.settings.models.Settings class method) (gufe.settings.models.SettingsBaseModel class method) (gufe.settings.models.ThermoSettings class method) values() (gufe.chemicalsystem.ChemicalSystem method) version_gufe (gufe.archival.AlchemicalArchive property) view_3d() (gufe.mapping.ligandatommapping.LigandAtomMapping method) VoltsQuantity (in module gufe.settings.typing) W with_annotations() (gufe.mapping.ligandatommapping.LigandAtomMapping method) with_traceback() (gufe.components.errors.ComponentValidationError method) (gufe.mapping.errors.AtomMappingError method) (gufe.protocols.errors.ExecutionInterrupt method) (gufe.protocols.errors.GufeProtocolError method) (gufe.protocols.errors.MissingUnitResultError method) (gufe.protocols.errors.ProtocolDAGError method) (gufe.protocols.errors.ProtocolDAGExecutionError method) (gufe.protocols.errors.ProtocolDAGResultError method) (gufe.protocols.errors.ProtocolUnitExecutionError method) (gufe.protocols.errors.ProtocolUnitFailureError method) (gufe.protocols.errors.ProtocolValidationError method) (gufe.storage.errors.ChangedExternalResourceError method) (gufe.storage.errors.ExternalResourceError method) (gufe.storage.errors.MissingExternalResourceError method) Z zfill() (gufe.tokenization.GufeKey method)