annotate ob_addh.py @ 5:8302ab092300 draft default tip

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

#!/usr/bin/env python
"""
    Input:  Molecule file
    Output: Molecule file with hydrogen atoms added at the target pH.
"""
import argparse
import sys

from openbabel import openbabel, pybel

openbabel.obErrorLog.StopLogging()


def parse_command_line(argv):
    parser = argparse.ArgumentParser()
    parser.add_argument("--iformat", type=str, default="sdf", help="input file format")
    parser.add_argument(
        "-i", "--input", type=str, required=True, help="input file name"
    )
    parser.add_argument(
        "-o", "--output", type=str, required=True, help="output file name"
    )
    parser.add_argument(
        "--polar",
        action="store_true",
        default=False,
        help="Add hydrogen atoms only to polar atoms",
    )
    parser.add_argument(
        "--pH", type=float, default="7.4", help="Specify target pH value"
    )
    return parser.parse_args()


def addh(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.removeh()
            mol.OBMol.AddHydrogens(args.polar, True, args.pH)
            outfile.write(mol)
    outfile.close()


def __main__():
    """
    Add hydrogen atoms at a certain pH value
    """
    args = parse_command_line(sys.argv)
    addh(args)


if __name__ == "__main__":
    __main__()