annotate ob_genProp.py @ 14:d7f0ca1f2669 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"

#!/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__()