Mercurial > repos > bgruening > openbabel_remsmall
diff ob_genProp.py @ 0:2704d4017b13 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author | bgruening |
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date | Sat, 20 May 2017 08:39:53 -0400 |
parents | |
children | aebc671bae78 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ob_genProp.py Sat May 20 08:39:53 2017 -0400 @@ -0,0 +1,52 @@ +#!/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 sys, os +import argparse +import openbabel +openbabel.obErrorLog.StopLogging() +import pybel +import cheminfolib + + +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__()