gemd.entity.bounds.molecular_structure_bounds module

Bounds a molecular structure to be a valid representation.

In the future, this may include substructural restrictions.

class gemd.entity.bounds.molecular_structure_bounds.MolecularStructureBounds

Molecular bounds, with no component or substructural restrictions (yet).

as_dict()

Convert bounds to a dictionary.

static build(d: Mapping[str, Any]) → DictSerializableType

Build an object from a JSON dictionary.

This differs from from_dict in that the values themselves may also be dictionaries corresponding to serialized DictSerializable objects.

contains(bounds: Union[BaseBounds, BaseValueType]) → bool

Check if another bounds or value object is contained by this bounds.

The other object must also be or type Molecular. There are no other conditions at this time.

Parameters: bounds (BaseBounds or BaseValue) – Other bounds or value object to check. If it’s a Value object, check against the smallest compatible bounds, as returned by the Value’s _to_bounds() method.
Returns: True if the other bounds is contained by this bounds.
Return type: bool

dump() → Dict[str, Any]

Convert the object to a JSON dictionary, so that every entry is serialized.

Uses the json encoder client, so objects with uids are converted to LinkByUID dictionaries.

classmethod from_dict(d: Mapping[str, Any]) → DictSerializableType

Reconstitute the object from a dictionary.

Parameters: d (dict) – The object as a dictionary of key-value pairs that correspond to the object’s fields.
Returns: The deserialized object.
Return type: DictSerializable

union(*others: Union[MolecularBoundsType, MolecularValueType]) → MolecularBoundsType

Return the union of this bounds and other bounds.

The others list must also be Molecular Structure Bounds or Values.

Parameters: others (MolecularStructureBounds or MolecularValue) – Other bounds or value objects to include.
Returns: The union of this bounds and the passed bounds. If they’re Value objects, increase by the smallest compatible bounds, as returned by the value’s _to_bounds() method.
Return type: MolecularStructureBounds

update(*others: Union[MolecularBoundsType, MolecularValueType])

Update this bounds to include other bounds.

The others list must also be Molecular Structure Bounds or Values.

Parameters: others (MolecularStructureBounds or MolecularValue) – Other bounds or value objects to include. If they’re Value objects, increase by the smallest compatible bounds, as returned by the value’s _to_bounds() method.