def set_atomic_charges(
mol: rdkit.Chem.rdchem.Mol,
atomic_numbers: Iterable[int],
atomic_valence_electrons,
BO_valences,
BO_matrix,
mol_charge,
) -> rdkit.Chem.rdchem.Mol:
q = 0
for i, atom in enumerate(atomic_numbers):
a = mol.GetAtomWithIdx(i)
charge = _get_atomic_charge(atom, atomic_valence_electrons[atom],
BO_valences[i])
q += charge
if atom == 6:
number_of_single_bonds_to_C = list(BO_matrix[i, :]).count(1)
if number_of_single_bonds_to_C == 2 and BO_valences[i] == 2:
q += 1
charge = 0
if number_of_single_bonds_to_C == 3 and q + 1 < mol_charge:
q += 2
charge = 1
if abs(charge) > 0:
a.SetFormalCharge(int(charge))
mol = _clean_charges(mol)
return mol
def set_atomic_radicals(
mol: rdkit.Chem.rdchem.Mol,
atomic_numbers: Iterable[int],
atomic_valence_electrons,
BO_valences,
) -> rdkit.Chem.rdchem.Mol:
# The number of radical electrons = absolute atomic charge
for i, atom in enumerate(atomic_numbers):
a = mol.GetAtomWithIdx(i)
charge = _get_atomic_charge(atom, atomic_valence_electrons[atom],
BO_valences[i])
if abs(charge) > 0:
a.SetNumRadicalElectrons(abs(int(charge)))
return mol