annotate ob_remIons.py @ 13:417845394cdf draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"

#!/usr/bin/env python
"""
    Input: molecular input file.
    Output: Molecule file with removed ions and fragments.
    Copyright 2012, Bjoern Gruening and Xavier Lucas
"""
import argparse

from openbabel import openbabel, pybel
openbabel.obErrorLog.StopLogging()


def parse_command_line():
    parser = argparse.ArgumentParser()
    parser.add_argument('-iformat', default='sdf', help='input file format')
    parser.add_argument('-i', '--input', required=True, help='input file name')
    parser.add_argument('-o', '--output', required=True, help='output file name')
    return parser.parse_args()


def remove_ions(args):
    outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
    for mol in pybel.readfile(args.iformat, args.input):
        if mol.OBMol.NumHvyAtoms() > 5:
            mol.OBMol.StripSalts(0)
            if 'inchi' in mol.data:
                del mol.data['inchi']  # remove inchi cache so modified mol is saved
            # Check if new small fragments have been created and remove them
            if mol.OBMol.NumHvyAtoms() > 5:
                outfile.write(mol)
    outfile.close()


def __main__():
    """
        Remove any counterion and delete any fragment but the largest one for each molecule.
    """
    args = parse_command_line()
    remove_ions(args)


if __name__ == "__main__":
    __main__()