BondingDoc

class emmet.core.bonds.BondingDoc(**data)

Bases: PropertyDoc

Structure graphs representing chemical bonds calculated from structure using near neighbor strategies as defined in pymatgen.

Parameters:

  • builder_meta (EmmetMeta | None)

  • nsites (int | None)

  • elements (list[Annotated[ElementTypeVar, BeforeValidator(func=~emmet.core.types.pymatgen_types.element_adapter.<lambda>, json_schema_input_type=PydanticUndefined), WrapSerializer(func=~emmet.core.types.pymatgen_types.element_adapter.<lambda>, return_type=str, when_used=always)]] | None)

  • nelements (int | None)

  • composition (Annotated[CompositionTypeVar, BeforeValidator(func=~emmet.core.types.pymatgen_types.composition_adapter.<lambda>, json_schema_input_type=PydanticUndefined), WrapSerializer(func=~emmet.core.types.pymatgen_types.composition_adapter.<lambda>, return_type=dict[str, float], when_used=always)] | None)

  • composition_reduced (Annotated[CompositionTypeVar, BeforeValidator(func=~emmet.core.types.pymatgen_types.composition_adapter.<lambda>, json_schema_input_type=PydanticUndefined), WrapSerializer(func=~emmet.core.types.pymatgen_types.composition_adapter.<lambda>, return_type=dict[str, float], when_used=always)] | None)

  • formula_pretty (str | None)

  • formula_anonymous (str | None)

  • chemsys (str | None)

  • volume (float | None)

  • density (float | None)

  • density_atomic (float | None)

  • symmetry (SymmetryData | None)

  • material_id (Annotated[MPID | AlphaID, BeforeValidator(func=~emmet.core.types.typing._fault_tolerant_id_serde, json_schema_input_type=PydanticUndefined), PlainSerializer(func=~emmet.core.types.typing.<lambda>, return_type=PydanticUndefined, when_used=always)] | None)

  • deprecated (bool)

  • deprecation_reasons (list[DeprecationMessage | str] | None)

  • last_updated (Annotated[datetime, BeforeValidator(func=~emmet.core.utils.convert_datetime, json_schema_input_type=PydanticUndefined)])

  • origins (list[PropertyOrigin] | None)

  • warnings (list[str])

  • structure (Annotated[Annotated[StructureTypeVar, BeforeValidator(func=~emmet.core.types.pymatgen_types.structure_adapter.pop_empty_structure_keys, json_schema_input_type=PydanticUndefined), WrapSerializer(func=~emmet.core.types.pymatgen_types.structure_adapter.<lambda>, return_type=~emmet.core.types.pymatgen_types.structure_adapter.TypedStructureDict, when_used=always)] | None, SkipJsonSchema()])

  • property_name (str)

  • structure_graph (Annotated[StructureGraphTypeVar, BeforeValidator(func=~emmet.core.types.pymatgen_types.structure_graph_adapter.pop_empty_graph_keys, json_schema_input_type=PydanticUndefined), WrapSerializer(func=~emmet.core.types.pymatgen_types.structure_graph_adapter.<lambda>, return_type=~emmet.core.types.pymatgen_types.structure_graph_adapter.TypedStructureGraphDict, when_used=always)])

  • method (str)

  • bond_types (dict[str, list[float]])

  • bond_length_stats (TypedBondLengthStatsDict)

  • coordination_envs (list[str])

  • coordination_envs_anonymous (list[str])

classmethod from_structure(structure, material_id, preferred_methods=('CrystalNN', 'MinimumDistanceNN'), **kwargs)

Calculate

Parameters:

  • structure (Structure) – ideally an oxidation state-decorated structure

  • material_id (str | MPID) – mpid

  • preferred_methods (tuple[str | NearNeighbors, ...]) – list of strings of NearNeighbor classes or NearNeighbor instances

  • deprecated – whether source material is or is not deprecated

  • kwargs – to pass to PropertyDoc

Return type:

Optional[Self]

Returns:

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].