Mercurial > repos > bgruening > openbabel_remove_protonation_state

annotate ob_addh.py @ 14:e376ba0fcde0 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 20:34:01 +0000
parents b578d0c101cd
children 22a866858b81
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1 #!/usr/bin/env python
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2 """
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3 Input: Molecule file
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4 Output: Molecule file with hydrogen atoms added at the target pH.
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5 """
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6 import argparse
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b578d0c101cd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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7 import sys
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bf4e668b6690 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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bf4e668b6690 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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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(argv):
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 parser = argparse.ArgumentParser()
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b578d0c101cd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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15 parser.add_argument('--iformat', type=str, default='sdf', help='input file format')
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0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 parser.add_argument('-i', '--input', type=str, required=True, help='input file name')
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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17 parser.add_argument('-o', '--output', type=str, required=True, help='output file name')
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18 parser.add_argument('--polar', action="store_true", default=False, help='Add hydrogen atoms only to polar atoms')
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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19 parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value')
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20 return parser.parse_args()
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23 def addh(args):
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24 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
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25 for mol in pybel.readfile(args.iformat, args.input):
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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26 if mol.OBMol.NumHvyAtoms() > 5:
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27 mol.removeh()
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28 mol.OBMol.AddHydrogens(args.polar, True, args.pH)
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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29 outfile.write(mol)
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30 outfile.close()
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33 def __main__():
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34 """
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35 Add hydrogen atoms at a certain pH value
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36 """
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37 args = parse_command_line(sys.argv)
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38 addh(args)
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41 if __name__ == "__main__":
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42 __main__()