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_utils

Utility and helper functions.

parse_assemblies(instance)

Parse assemblies properties from the OPTIMADEStructureResource entity into "proper" OPT StructureResource 'Assembly's.

Source code in oteapi_optimade/_utils.py 
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def parse_assemblies(instance: dlite.Instance | dict[str, Any]) -> list[dict[str, Any]]:
    """Parse assemblies properties from the OPTIMADEStructureResource entity into "proper" OPT
    StructureResource 'Assembly's."""
    if not _check_correct_entity(instance, "OPTIMADEStructureResource"):
        raise ValueError(
            "Entity for the instance is not an OPTIMADEStructureResource entity."
        )

    if isinstance(instance, dlite.Instance):
        instance = instance.asdict(single=True)

    if not isinstance(instance, dict):
        raise TypeError("Entity instance is not a dictionary.")

    assemblies: list[dict[str, Any]] = []

    for index in range(instance["dimensions"]["nassemblies"]):
        assemblies.append(
            {
                "sites_in_groups": [
                    [int(_) for _ in group.split(",")]
                    for group in instance["properties"]["assembly_sites_in_groups"][
                        index
                    ].split(";")
                ],
                "group_probabilities": [
                    float(_)
                    for _ in instance["properties"]["assembly_group_probabilities"][
                        index
                    ].split(",")
                ],
            }
        )

    return assemblies

parse_species(instance)

Parse species properties from the OPTIMADEStructureResource entity into "proper" OPT StructureResource Species.

Source code in oteapi_optimade/_utils.py 
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def parse_species(instance: dlite.Instance | dict[str, Any]) -> list[dict[str, Any]]:
    """Parse species properties from the OPTIMADEStructureResource entity into "proper" OPT
    StructureResource Species."""
    if not _check_correct_entity(instance, "OPTIMADEStructureResource"):
        raise ValueError(
            "Entity for the instance is not an OPTIMADEStructureResource entity."
        )

    if isinstance(instance, dlite.Instance):
        instance = instance.asdict(single=True)

    if not isinstance(instance, dict):
        raise TypeError("Entity instance is not a dictionary.")

    species: list[dict[str, Any]] = []

    for index in range(instance["dimensions"]["nspecies"]):
        # Required fields
        new_species = {
            "name": instance["properties"]["species_name"][index],
            "chemical_symbols": instance["properties"]["species_chemical_symbols"][
                index
            ].split(","),
            "concentration": [
                float(_)
                for _ in instance["properties"]["species_concentration"][index].split(
                    ","
                )
            ],
        }

        # Optional fields
        if mass := instance["properties"]["species_mass"][index]:
            new_species["mass"] = [float(_) for _ in mass.split(",")]

        if original_name := instance["properties"]["species_original_name"][index]:
            new_species["original_name"] = original_name

        if attached := instance["properties"]["species_attached"][index]:
            new_species["attached"] = attached.split(",")

            if "species_nattached" not in instance["properties"]:
                raise ValueError(
                    "species_attached is present, but species_nattached is missing."
                )

            new_species["nattached"] = [
                int(_)
                for _ in instance["properties"]["species_nattached"][index].split(",")
            ]

        species.append(new_species)

    return species