Mercurial > repos > bgruening > openbabel_genprop
view ob_genProp.py @ 13:417845394cdf draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author | bgruening |
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date | Mon, 19 Oct 2020 14:46:54 +0000 |
parents | a72ae2711a97 |
children | 50eaae9df8d3 |
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#!/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__()