dgllife.utils.get_mol_3d_coordinates¶

dgllife.utils.get_mol_3d_coordinates(mol)[source]¶

Get 3D coordinates of the molecule.

This function requires that molecular conformation has been initialized.

Parameters: mol (rdkit.Chem.rdchem.Mol) – RDKit molecule instance.
Returns: The 3D coordinates of atoms in the molecule. N for the number of atoms in the molecule. For failures in getting the conformations, None will be returned.
Return type: numpy.ndarray of shape (N, 3) or None

Examples

An error will occur in the example below since the molecule object does not carry conformation information.

>>> from rdkit import Chem
>>> from dgllife.utils import get_mol_3d_coordinates

>>> mol = Chem.MolFromSmiles('CCO')

Below we give a working example based on molecule conformation initialized from calculation.

>>> from rdkit.Chem import AllChem
>>> AllChem.EmbedMolecule(mol)
>>> AllChem.MMFFOptimizeMolecule(mol)
>>> coords = get_mol_3d_coordinates(mol)
>>> print(coords)
array([[ 1.20967478, -0.25802181,  0.        ],
       [-0.05021255,  0.57068079,  0.        ],
       [-1.15946223, -0.31265898,  0.        ]])