When using molecules.rd_mol_to_ob_mol to convert an RDKit molecule to a OpenBabel molecule, aromaticity information seem to be lost, which results in erroneous atom types when gridding.
from molecules import rd_mol_to_ob_mol
from rdkit import Chem
from rdkit.Chem import AllChem
from openbabel import pybel
rdmol = Chem.MolFromSmiles("c1ccccc1")
AllChem.EmbedMolecule(rdmol)
w = Chem.SDWriter('rdmol.sdf')
w.write(rdmol)
w.close()
obmol = rd_mol_to_ob_mol(rdmol)
pybel.Molecule(obmol).write("sdf", "obmol.sdf", overwrite=True)
When using
molecules.rd_mol_to_ob_mol
to convert an RDKit molecule to a OpenBabel molecule, aromaticity information seem to be lost, which results in erroneous atom types when gridding.