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ANONYMOUS_ELEMENTS = tuple(itertools.islice(anonymous_element_generator(), 150)) module-attribute

Returns the first 150 values of the anonymous element generator.

ATOMIC_NUMBERS = {} module-attribute

CHEMICAL_FORMULA_REGEXP = '(^$)|^([A-Z][a-z]?([2-9]|[1-9]\\d+)?)+$' module-attribute

CHEMICAL_SYMBOLS = ['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og'] module-attribute

ELEMENT_SYMBOLS_PATTERN = '(' + '|'.join(CHEMICAL_SYMBOLS) + ')' module-attribute

EXTENDED_CHEMICAL_SYMBOLS_PATTERN = '(' + '|'.join(CHEMICAL_SYMBOLS + EXTRA_SYMBOLS) + ')' module-attribute

EXTRA_SYMBOLS = ['X', 'vacancy'] module-attribute

OPTIMADE_SCHEMA_EXTENSION_KEYS = ['support', 'queryable', 'unit', 'sortable'] module-attribute

OPTIMADE_SCHEMA_EXTENSION_PREFIX = 'x-optimade-' module-attribute

SEMVER_PATTERN = '^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$' module-attribute

SupportLevel

Bases: Enum

OPTIMADE property/field support levels

Source code in optimade/models/utils.py 
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class SupportLevel(Enum):
    """OPTIMADE property/field support levels"""

    MUST = "must"
    SHOULD = "should"
    OPTIONAL = "optional"

MUST = 'must' class-attribute instance-attribute

OPTIONAL = 'optional' class-attribute instance-attribute

SHOULD = 'should' class-attribute instance-attribute

OptimadeField(default=PydanticUndefined, *, support=None, queryable=None, unit=None, **kwargs)

A wrapper around pydantic.Field that adds OPTIMADE-specific field paramters queryable, support and unit, indicating the corresponding support level in the specification and the physical unit of the field.

Parameters:

Name Type Description Default
support Optional[Union[str, SupportLevel]]

The support level of the field itself, i.e. whether the field can be null or omitted by an implementation.

 None
queryable Optional[Union[str, SupportLevel]]

The support level corresponding to the queryablility of this field.

 None
unit Optional[str]

A string describing the unit of the field.

 None

Returns:

Type Description
Any

The pydantic field with extra validation provided by StrictField.
Source code in optimade/models/utils.py 
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def OptimadeField(
    default: "Any" = PydanticUndefined,
    *,
    support: Optional[Union[str, SupportLevel]] = None,
    queryable: Optional[Union[str, SupportLevel]] = None,
    unit: Optional[str] = None,
    **kwargs,
) -> Any:
    """A wrapper around `pydantic.Field` that adds OPTIMADE-specific
    field paramters `queryable`, `support` and `unit`, indicating
    the corresponding support level in the specification and the
    physical unit of the field.

    Arguments:
        support: The support level of the field itself, i.e. whether the field
            can be null or omitted by an implementation.
        queryable: The support level corresponding to the queryablility
            of this field.
        unit: A string describing the unit of the field.

    Returns:
        The pydantic field with extra validation provided by [`StrictField`][optimade.models.utils.StrictField].

    """

    # Collect non-null keyword arguments to add to the Field schema
    if unit is not None:
        kwargs["unit"] = unit

    if queryable is not None:
        if isinstance(queryable, str):
            queryable = SupportLevel(queryable.lower())
        kwargs["queryable"] = queryable

    if support is not None:
        if isinstance(support, str):
            support = SupportLevel(support.lower())
        kwargs["support"] = support

    return StrictField(default, **kwargs)

StrictField(default=PydanticUndefined, *, description=None, **kwargs)

A wrapper around pydantic.Field that does the following:

  • Forbids any "extra" keys that would be passed to pydantic.Field, except those used elsewhere to modify the schema in-place, e.g. "uniqueItems", "pattern" and those added by OptimadeField, e.g. "unit", "queryable" and "sortable".
  • Emits a warning when no description is provided.

Parameters:

Name Type Description Default
default Any

The only non-keyword argument allowed for Field.

 PydanticUndefined
description Optional[str]

The description of the Field; if this is not specified then a UserWarning will be emitted.

 None
**kwargs Any

Extra keyword arguments to be passed to Field.

 {}

Raises:

Type Description
RuntimeError

If **kwargs contains a key not found in the function signature of Field, or in the extensions used by models in this package (see above).

Returns:

Type Description
Any

The pydantic Field.
Source code in optimade/models/utils.py 
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def StrictField(
    default: "Any" = PydanticUndefined,
    *,
    description: Optional[str] = None,
    **kwargs: "Any",
) -> Any:
    """A wrapper around `pydantic.Field` that does the following:

    - Forbids any "extra" keys that would be passed to `pydantic.Field`,
      except those used elsewhere to modify the schema in-place,
      e.g. "uniqueItems", "pattern" and those added by OptimadeField, e.g.
      "unit", "queryable" and "sortable".
    - Emits a warning when no description is provided.

    Arguments:
        default: The only non-keyword argument allowed for Field.
        description: The description of the `Field`; if this is not
            specified then a `UserWarning` will be emitted.
        **kwargs: Extra keyword arguments to be passed to `Field`.

    Raises:
        RuntimeError: If `**kwargs` contains a key not found in the
            function signature of `Field`, or in the extensions used
            by models in this package (see above).

    Returns:
        The pydantic `Field`.

    """
    allowed_schema_and_field_keys = ["pattern"]

    allowed_keys = [
        "pattern",
        "uniqueItems",
    ] + OPTIMADE_SCHEMA_EXTENSION_KEYS
    _banned = [k for k in kwargs if k not in set(_PYDANTIC_FIELD_KWARGS + allowed_keys)]

    if _banned:
        raise RuntimeError(
            f"Not creating StrictField({default!r}, **{kwargs!r}) with "
            f"forbidden keywords {_banned}."
        )

    # Handle description
    if description is None:
        warnings.warn(
            f"No description provided for StrictField specified by {default!r}, "
            f"**{kwargs!r}."
        )
    else:
        kwargs["description"] = description

    # OPTIMADE schema extensions
    json_schema_extra: dict[str, Any] = kwargs.pop("json_schema_extra", {})

    # Go through all JSON Schema keys and add them to the json_schema_extra.
    for key in allowed_keys:
        if key not in kwargs:
            continue

        # If they are OPTIMADE schema extensions, add them with the OPTIMADE prefix.
        schema_key = (
            f"{OPTIMADE_SCHEMA_EXTENSION_PREFIX}{key}"
            if key in OPTIMADE_SCHEMA_EXTENSION_KEYS
            else key
        )

        for key_variant in (key, schema_key):
            if key_variant in json_schema_extra:
                if json_schema_extra.pop(key_variant) != kwargs[key]:
                    raise RuntimeError(
                        f"Conflicting values for {key} in json_schema_extra and kwargs."
                    )

        json_schema_extra[schema_key] = (
            kwargs[key] if key in allowed_schema_and_field_keys else kwargs.pop(key)
        )

    kwargs["json_schema_extra"] = json_schema_extra

    return Field(default, **kwargs)

anonymize_formula(formula)

Takes a string representation of a chemical formula of the form [A-Z][a-z]*[0-9]* (potentially with whitespace) and returns the OPTIMADE chemical_formula_anonymous representation, i.e., a reduced chemical formula comprising of element symbols drawn from A, B, C... ordered from largest proportion to smallest.

Returns:

Type Description
str

The anonymous chemical formula in the OPTIMADE representation.
Source code in optimade/models/utils.py 
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def anonymize_formula(formula: str) -> str:
    """Takes a string representation of a chemical formula of the form `[A-Z][a-z]*[0-9]*` (potentially with whitespace) and
    returns the OPTIMADE `chemical_formula_anonymous` representation, i.e., a reduced chemical formula comprising of element symbols
    drawn from A, B, C... ordered from largest proportion to smallest.

    Returns:
        The anonymous chemical formula in the OPTIMADE representation.

    """
    return _reduce_or_anonymize_formula(formula, alphabetize=False, anonymize=True)

anonymous_element_generator()

Generator that yields the next symbol in the A, B, Aa, ... Az naming scheme.

Source code in optimade/models/utils.py 
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def anonymous_element_generator() -> "Generator[str, None, None]":
    """Generator that yields the next symbol in the A, B, Aa, ... Az naming scheme."""
    from string import ascii_lowercase

    for size in itertools.count(1):
        for tuple_strings in itertools.product(ascii_lowercase, repeat=size):
            list_strings = list(tuple_strings)
            list_strings[0] = list_strings[0].upper()
            yield "".join(list_strings)

reduce_formula(formula)

Takes a string representation of a chemical formula of the form [A-Z][a-z]*[0-9]* (potentially with whitespace) and reduces it by the GCD of the proportion integers present in the formula, stripping any leftover "1" values.

Returns:

Type Description
str

The reduced chemical formula in the OPTIMADE representation.
Source code in optimade/models/utils.py 
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def reduce_formula(formula: str) -> str:
    """Takes a string representation of a chemical formula of the form `[A-Z][a-z]*[0-9]*` (potentially with whitespace) and
    reduces it by the GCD of the proportion integers present in the formula, stripping any leftover "1" values.

    Returns:
        The reduced chemical formula in the OPTIMADE representation.

    """
    return _reduce_or_anonymize_formula(formula, alphabetize=True, anonymize=False)