add_h.py

#!/usr/bin/env python3

__author__ = 'Pavel Polishchuk'


import argparse
import glob
from rdkit import Chem


def main():
    parser = argparse.ArgumentParser(description='Add hydrogens to input files.')
    parser.add_argument('-i', '--input', metavar='FILENAME', nargs='+', required=True,
                        help='input MOL/SDF files. Multiple files can be supplied. MOL files are modified in place. '
                             'SDF files result in new SDF files with suffix _H in file name.')

    args = parser.parse_args()

    for path in args.input:
        for fname in glob.glob(path):

            if fname.endswith('.mol'):
                mol = Chem.MolFromMolFile(fname, removeHs=False)
                mol = Chem.AddHs(mol, addCoords=True)
                Chem.MolToMolFile(mol, fname)

            if fname.endswith('.sdf'):
                mols = [Chem.AddHs(mol, addCoords=True) for mol in Chem.SDMolSupplier(fname, removeHs=False) if mol is not None]
                w = Chem.SDWriter(fname[:-4] + '_H.sdf')
                for mol in mols:
                    w.write(mol)
                w.close()


if __name__ == '__main__':
    main()