def compute_charge_dictionary(molecule):
"""Create a dictionary with partial charges for each atom in the molecule.
This function assumes that the charges for the molecule are
already computed (it can be done with
rdkit_util.compute_charges(molecule))
"""
charge_dictionary = {}
for i, atom in enumerate(molecule.GetAtoms()):
charge_dictionary[i] = get_partial_charge(atom)
return charge_dictionary
def is_salt_bridge(atom_i, atom_j):
"""Check if two atoms have correct charges to form a salt bridge"""
if np.abs(2.0 - np.abs(
get_partial_charge(atom_i) - get_partial_charge(atom_j))) < 0.01:
return True
return False
def test_get_partial_charge(self):
from rdkit import Chem
mol = Chem.MolFromSmiles("CC")
atom = mol.GetAtoms()[0]
partial_charge = get_partial_charge(atom)
assert partial_charge == 0