def test_compute_charges(self):
current_dir = os.path.dirname(os.path.realpath(__file__))
ligand_file = os.path.join(current_dir, "../../dock/tests/1jld_ligand.sdf")
xyz, mol = rdkit_utils.load_molecule(
ligand_file, calc_charges=False, add_hydrogens=True)
rdkit_utils.compute_charges(mol)
has_a_charge = False
for atom_idx in range(mol.GetNumAtoms()):
atom = mol.GetAtoms()[atom_idx]
value = atom.GetProp(str("_GasteigerCharge"))
if value != 0:
has_a_charge = True
assert has_a_charge
def get_mol_subset(
coords: np.ndarray, mol: Union[RDKitMol, MolecularFragment],
atom_indices_to_keep: List[int]
) -> Tuple[np.ndarray, MolecularFragment]:
"""Strip a subset of the atoms in this molecule
Parameters
----------
coords: np.ndarray
Must be of shape (N, 3) and correspond to coordinates of mol.
mol: RDKit Mol or MolecularFragment
The molecule to strip
atom_indices_to_keep: list
List of the indices of the atoms to keep. Each index is a unique
number between `[0, N)`.
Returns
-------
Tuple[np.ndarray, MolecularFragment]
A tuple of `(coords, mol_frag)` where `coords` is a numpy array of
coordinates with hydrogen coordinates. `mol_frag` is a `MolecularFragment`.
Note
----
This function requires RDKit to be installed.
"""
try:
from rdkit import Chem
except ModuleNotFoundError:
raise ValueError("This function requires RDKit to be installed.")
indexes_to_keep = []
atoms_to_keep = []
# Compute partial charges on molecule if RDKit Mol
if isinstance(mol, Chem.Mol):
compute_charges(mol)
atoms = list(mol.GetAtoms())
for index in atom_indices_to_keep:
indexes_to_keep.append(index)
atoms_to_keep.append(atoms[index])
coords = coords[indexes_to_keep]
mol_frag = MolecularFragment(atoms_to_keep, coords)
return coords, mol_frag