Mercurial > repos > bgruening > prepare_ligands_for_docking
comparison change_title_to_metadata_value.py @ 0:06340f46ecb8 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
author | bgruening |
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date | Fri, 10 May 2019 08:55:09 -0400 |
parents | |
children | b8838a9aa31a |
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-1:000000000000 | 0:06340f46ecb8 |
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1 #!/usr/bin/env python | |
2 # -*- coding: UTF-8 -*- | |
3 | |
4 """ | |
5 Change the title from a molecule file to metadata | |
6 value of a given-id of the same molecule file. | |
7 """ | |
8 | |
9 import os | |
10 import sys | |
11 import argparse | |
12 import openbabel | |
13 openbabel.obErrorLog.StopLogging() | |
14 import pybel | |
15 | |
16 | |
17 def main(): | |
18 parser = argparse.ArgumentParser( | |
19 description="Change the title from a molecule file to metadata \ | |
20 value of a given-id of the same molecule file.", | |
21 ) | |
22 parser.add_argument('--infile', '-i', | |
23 required=True, help="path to the input file") | |
24 parser.add_argument('--outfile', '-o', | |
25 required=True, help="path to the output file") | |
26 parser.add_argument('--key', '-k', | |
27 required=True, help="the metadata key from the sdf file which should inlcude the new title") | |
28 | |
29 args = parser.parse_args() | |
30 | |
31 output = pybel.Outputfile("sdf", args.outfile, overwrite=True) | |
32 | |
33 for mol in pybel.readfile("sdf", args.infile): | |
34 if args.key in mol.data: | |
35 mol.title = mol.data[args.key] | |
36 output.write( mol ) | |
37 | |
38 output.close() | |
39 | |
40 | |
41 if __name__ == "__main__": | |
42 main() | |
43 |