def get_charge(mol, property_name, do_charge):
from rdkit.Chem import AllChem as Chem
err = 0
# partial charges
if do_charge is False:
err = check_mol(mol, property_name, do_charge)
if err == 0:
# prepares molecule
mol = Chem.RemoveHs(mol)
n_at = mol.GetNumAtoms()
# takes properties
list_prop = mol.GetPropsAsDict()
# extracts the property according to the set name
string_values = list_prop[property_name]
string_values = string_values.split("\n")
w = np.asarray(map(float, string_values))
else:
mol = Chem.AddHs(mol)
n_at = mol.GetNumAtoms()
w = np.ones((n_at, 1)) / n_at
# same format as previous calculation
w = np.asarray(map(float, w))
property_name = 'equal_w'
err = 0
# extract properties
for atom in range(n_at):
mol.GetAtomWithIdx(atom).SetDoubleProp(property_name, w[atom])
mol = Chem.RemoveHs(mol)
# Gasteiger-Marsili Charges
elif (do_charge is True) and (err is 0):
Chem.ComputeGasteigerCharges(mol)
err = check_mol(mol, property_name, do_charge)
return mol, property_name, err
