Data

schemas.data.Data

Bases: ABC

Assists with updating data with atomistic schemas.

_get_field_value(key)

Retrieve the value of a field in the schema.

PARAMETER	DESCRIPTION
key	The key of the field to retrieve. Can use dot notation for nested attributes. TYPE: str

RETURNS	DESCRIPTION
Any	A tuple containing the keys, sub_model, and the current value of the field.

_set_field(key, value, separator='.')

Set a single field in the schema.

PARAMETER	DESCRIPTION
key	The key of the field to update. Can use dot notation for nested attributes. TYPE: str
value	The value to set for the specified field. TYPE: Any
separator	The string used to separate nested keys. TYPE: str DEFAULT: '.'

_trim_molecule_arrays(mol_index, schema_map)

Finalize arrays by trimming off the unused portions based on the current index.

PARAMETER	DESCRIPTION
mol_index	The current index up to which the arrays should be retained. TYPE: int
schema_map	A mapping of field keys to their cadence and other metadata. TYPE: dict[str, dict[str, str]]

_update_array(key, value, mol_index=0)

Update an array field in the schema, resizing if necessary.

PARAMETER	DESCRIPTION
key	The key of the array field to update. Can use dot notation for nested attributes. TYPE: str
value	The value to add to the array. TYPE: Any
mol_index	The current index for appending new values. TYPE: int DEFAULT: 0

RETURNS	DESCRIPTION
int	The updated molecule index after appending the new values.

RAISES	DESCRIPTION
TypeError	If the value is not a numpy array or cannot be converted to one.

update_atomistic(data, schema_map, mol_index=0)

Update the fields of the Schema instance with the provided data.

This method updates the attributes of the Schema instance based on the keys and values in the provided dictionary. The keys in the dictionary can represent nested fields using dot notation.

PARAMETER	DESCRIPTION
data	A dictionary containing the keys and values to update the EnsembleSchema instance. The keys can use dot notation to specify nested attributes. TYPE: dict[str, Any]
schema_map	A mapping of field keys to their cadence and other metadata. TYPE: dict[str, dict[str, str]]
mol_index	The current molecule index for updating array fields. TYPE: int DEFAULT: 0

RETURNS	DESCRIPTION
int	The updated molecule index after processing the input data.

Example

mol_schema = EnsembleSchema()
schema_map = mol_schema.get_schema_map()
data = {
    "qc.energy": -76.4,
    "system.coordinates": [[0.0, 0.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0]],
    "topology.bonds": [(0, 1), (0, 2)]
}
molecule.update(data, schema_map)

RAISES	DESCRIPTION
AttributeError	If a specified attribute does not exist in the schema.
ValueError	If the cadence is unknown.

Notes

• The method supports updating nested attributes by splitting keys on the dot ('.') character.
• If a key does not use dot notation, it will update the top-level attribute directly.