annotate ob_genProp.py @ 15:7b6fd1c273cd 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: Physico-chemical properties are computed and stored as metadata in the sdf output file.
    Copyright 2012, Bjoern Gruening and Xavier Lucas
"""
import argparse
import sys

import cheminfolib
import openbabel
from openbabel import pybel

openbabel.obErrorLog.StopLogging()


def parse_command_line(argv):
    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(
        "--oformat", default="sdf", choices=["sdf", "table"], help="output file format"
    )
    parser.add_argument(
        "--header",
        type=bool,
        help="Include the header as the first line of the output table",
    )
    parser.add_argument("-o", "--output", required=True, help="output file name")
    return parser.parse_args()


def compute_properties(args):
    if args.oformat == "sdf":
        outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
    else:
        outfile = open(args.output, "w")
        if args.header:
            mol = next(pybel.readfile(args.iformat, args.input))
            metadata = cheminfolib.get_properties_ext(mol)
            outfile.write(
                "%s\n" % "\t".join([cheminfolib.ColumnNames[key] for key in metadata])
            )

    for mol in pybel.readfile(args.iformat, args.input):
        if mol.OBMol.NumHvyAtoms() > 5:
            metadata = cheminfolib.get_properties_ext(mol)
            if args.oformat == "sdf":
                [
                    mol.data.update({cheminfolib.ColumnNames[key]: metadata[key]})
                    for key in metadata
                ]
                outfile.write(mol)
            else:
                outfile.write(
                    "%s\n" % ("\t".join([str(metadata[key]) for key in metadata]))
                )
    outfile.close()


def __main__():
    """
    Physico-chemical properties are computed and stored as metadata in the sdf output file
    """
    args = parse_command_line(sys.argv)
    compute_properties(args)


if __name__ == "__main__":
    __main__()