annotate ob_remIons.py @ 15:c5de6c19eb06 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

#!/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")
    parser.add_argument(
        "-idx",
        default=False,
        action="store_true",
        help="should output be an indexed text table? works only for inchi/smiles, otherwise is ignored",
    )
    return parser.parse_args()


def remove_ions(args):
    with open(args.output, "w") as outfile:
        for index, mol in enumerate(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

            mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else "\n"

            if args.idx and args.iformat in ["inchi", "smi"]:
                outfile.write(f"{index}\t{mol}")
            elif mol != "\n":
                outfile.write(f"{mol}")


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__()