Mercurial > repos > bgruening > openbabel_structure_distance_finder

annotate remove_protonation_state.py @ 4:2c5c7da26e08 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author bgruening
date Tue, 10 Nov 2020 20:40:06 +0000
parents 49242402887b
children 8302ab092300
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c066b5accacf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
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1 #!/usr/bin/env python
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2 """
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3 Input: molecular input file.
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4 Output: Molecule file with removed ions and fragments.
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5 Copyright 2013, Bjoern Gruening and Xavier Lucas
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6 """
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7 import argparse
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9 from openbabel import openbabel, pybel
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10 openbabel.obErrorLog.StopLogging()
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13 def parse_command_line():
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14 parser = argparse.ArgumentParser()
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15 parser.add_argument('--iformat', default='sdf', help='input file format')
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16 parser.add_argument('-i', '--input', required=True, help='input file name')
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17 parser.add_argument('-o', '--output', required=True, help='output file name')
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18 return parser.parse_args()
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21 def remove_protonation(args):
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22 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
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23 for mol in pybel.readfile(args.iformat, args.input):
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24 [atom.OBAtom.SetFormalCharge(0) for atom in mol.atoms]
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25 if 'inchi' in mol.data:
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26 del mol.data['inchi'] # remove inchi cache so modified mol is saved
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27 outfile.write(mol)
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28 outfile.close()
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31 def __main__():
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32 """
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33 Remove any protonation state from each atom in each molecule.
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34 """
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35 args = parse_command_line()
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36 remove_protonation(args)
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39 if __name__ == "__main__":
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40 __main__()