class matlantis_features.atoms.MatlantisAtoms(atoms: Atoms)#

Bases: object

MatlantisAtoms object is a collection of atoms used in matlantis-features and wraps ase.Atoms class.

__init__(atoms: Atoms)#

Initialize an instance.

Parameters

atoms (ASEAtoms) – A collection of atoms specified by AseAtoms.

property ase_atoms: Atoms#

Get the AseAtoms corresponding to the object.

Returns

The AseAtoms corresponding to the object.

Return type

ASEAtoms

copy() → MatlantisAtoms#

Get a copy of the MatlantisAtoms object.

Returns

Copy of the atoms.

Return type

MatlantisAtoms

classmethod from_ase_atoms(atoms: Atoms) → MatlantisAtoms#

A classmethod to convert ASEAtoms to MatlantisAtoms.

Parameters

atoms (ASEAtoms) – AseAtoms object to convert.

Returns

MatlantisAtoms corresponding to the input AseAtoms.

Return type

MatlantisAtoms

classmethod from_dict(res: Dict[str, Any]) → MatlantisAtoms#

Construct a MatlantisAtoms object from serialized dict.

Parameters

res (dict[str, Any]) – A dict containing a serialized MatlantisAtoms from to_dict().

Returns

The deserialized object from provided dict.

Return type

MatlantisAtoms

classmethod from_file(file: Union[str, Path]) → MatlantisAtoms#

A classmethod to get MatlantisAtoms from a file using ase.io.read function.

Parameters

file (str or pathlib.Path) – A path to file to convert.

Returns

MatlantisAtoms corresponding to the input file.

Return type

MatlantisAtoms

classmethod from_rdkit_mol(mol: Mol) → MatlantisAtoms#

A classmethod to get MatlantisAtoms from an rdkit.Chem.Mol object. The positions of atoms should be set.

Parameters

mol (Mol) – An rdkit.Chem.Mol object to convert.

Returns

MatlantisAtoms corresponding to the input Mol object.

Return type

MatlantisAtoms

classmethod from_smiles(smiles: str, method: str = ‘etkdg_v2’, seed: int = -1) → MatlantisAtoms#

A classmethod to get MatlantisAtoms from a SMILES.

Parameters

  • smiles (str) – A SMILES string to convert.

  • method (str, optional) – An algorithm for position embedding. The algorithm can be selected from ["etkdg_v2", "etkdg", "etdg", "kdg", "2d"]. Defaults to ‘etkdg_v2’.

  • seed (int, optional) – A random seed for position embedding. Defaults to (-1).

Returns

MatlantisAtoms corresponding to the input SMILES.

Return type

MatlantisAtoms

property numbers: ndarray#

Get the array of atomic numbers of the atoms.

Returns

The array of atomic numbers of the atoms.

Return type

np.ndarray

property positions: ndarray#

Get the array of coordinates of the atoms.

Returns

The array of coordinates of the atoms.

Return type

np.ndarray

rotate_atoms_to_upper() → None#

Rotate the MatlantisAtoms inplace to make its cell a upper triangular matrix.

to_dict() → Dict[str, Any]#

Dictionary representation of the MatlantisAtoms.

Returns

The dictionary containing the serialized MatlantisAtoms.

Return type

dict[str, Any]