Mercurial > repos > bgruening > openbabel_remsmall
comparison 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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-1:000000000000 | 0:2704d4017b13 |
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1 #!/usr/bin/env python | |
2 """ | |
3 Input: Molecular input file. | |
4 Output: Physico-chemical properties are computed and stored as metadata in the sdf output file. | |
5 Copyright 2012, Bjoern Gruening and Xavier Lucas | |
6 """ | |
7 import sys, os | |
8 import argparse | |
9 import openbabel | |
10 openbabel.obErrorLog.StopLogging() | |
11 import pybel | |
12 import cheminfolib | |
13 | |
14 | |
15 def parse_command_line(argv): | |
16 parser = argparse.ArgumentParser() | |
17 parser.add_argument('--iformat', default='sdf' , help='input file format') | |
18 parser.add_argument('-i', '--input', required=True, help='input file name') | |
19 parser.add_argument('--oformat', default='sdf', choices = ['sdf', 'table'] , help='output file format') | |
20 parser.add_argument('--header', type=bool, help='Include the header as the first line of the output table') | |
21 parser.add_argument('-o', '--output', required=True, help='output file name') | |
22 return parser.parse_args() | |
23 | |
24 def compute_properties(args): | |
25 if args.oformat == 'sdf': | |
26 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) | |
27 else: | |
28 outfile = open(args.output, 'w') | |
29 if args.header: | |
30 mol = next(pybel.readfile(args.iformat, args.input)) | |
31 metadata = cheminfolib.get_properties_ext(mol) | |
32 outfile.write( '%s\n' % '\t'.join( [ cheminfolib.ColumnNames[key] for key in metadata ] ) ) | |
33 | |
34 for mol in pybel.readfile(args.iformat, args.input): | |
35 if mol.OBMol.NumHvyAtoms() > 5: | |
36 metadata = cheminfolib.get_properties_ext(mol) | |
37 if args.oformat == 'sdf': | |
38 [ mol.data.update( { cheminfolib.ColumnNames[key] : metadata[key] } ) for key in metadata ] | |
39 outfile.write(mol) | |
40 else: | |
41 outfile.write( '%s\n' % ('\t'.join( [ str(metadata[key]) for key in metadata ] ) ) ) | |
42 outfile.close() | |
43 | |
44 def __main__(): | |
45 """ | |
46 Physico-chemical properties are computed and stored as metadata in the sdf output file | |
47 """ | |
48 args = parse_command_line(sys.argv) | |
49 compute_properties(args) | |
50 | |
51 if __name__ == "__main__" : | |
52 __main__() |