Import cclib files to RDKit molecules

cclib-rdkit.py

#!/usr/bin/env python

import sys
import os

import cclib
from cclib.parser import ccopen

from rdkit import Chem
try:
    from rdkit.Chem import rdDetermineBonds
except ImportError:
    exit('This script requires RDKit version 2022.09 or later')

# repeat through all the files on the command-line
# we can change this to use the glob module as well
#  e.g., find all the files in a set of folders
for argument in sys.argv[1:]:
    filename, extension = os.path.splitext(argument)

    try:
        parser = ccopen(argument)
        data = parser.parse()
    except:
        print("Error importing %s" % argument)
        continue

    # okay, now let's build the RDKit molecule
    mol = Chem.RWMol()
    # we'll need space for the 3D coordinates
    conformer = Chem.Conformer(len(data.atomnos))
    for atom in data.atomnos:
        mol.AddAtom(Chem.Atom(int(atom)))
    for i in range(len(data.atomcoords[-1])):
        conformer.SetAtomPosition(i, data.atomcoords[-1][i])
    mol.AddConformer(conformer)
    # now the new bond connectivity and bond orders
    bonded_mol = Chem.Mol(mol)
    rdDetermineBonds.DetermineConnectivity(bonded_mol)
    rdDetermineBonds.DetermineBondOrders(bonded_mol, data.charge)
    # and finally the stereochemistry
    Chem.AssignStereochemistryFrom3D(bonded_mol)

    # print the SMILES
    smi = Chem.MolToSmiles(bonded_mol)
    escape = f"Charge: {data.charge} Spin: {data.mult}"
    print(f"From file {argument} I found SMILES {smi}")