Mercurial > repos > bgruening > openbabel_obgrep

annotate ob_addh.py @ 5:50dc8ca09a50 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 3ba9268697beb4827bd9e8e639e70166f224cb8b
author bgruening
date Mon, 03 Sep 2018 16:40:06 -0400
parents b0311f002a5f
children 78640d0127ce
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b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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diff changeset
1 #!/usr/bin/env python
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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2 """
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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3 Input: Molecule file
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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4 Output: Molecule file with hydrogen atoms added at the target pH.
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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5 """
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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6 import sys, os
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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7 import argparse
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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8 import openbabel
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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9 openbabel.obErrorLog.StopLogging()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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10 import pybel
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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11
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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12 def parse_command_line(argv):
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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13 parser = argparse.ArgumentParser()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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14 parser.add_argument('--iformat', type=str, default='sdf' , help='input file format')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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15 parser.add_argument('-i', '--input', type=str, required=True, help='input file name')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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16 parser.add_argument('-o', '--output', type=str, required=True, help='output file name')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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17 parser.add_argument('--polar', action="store_true", default=False, help='Add hydrogen atoms only to polar atoms')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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18 parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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19 return parser.parse_args()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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21 def addh(args):
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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22 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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23 for mol in pybel.readfile(args.iformat, args.input):
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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24 if mol.OBMol.NumHvyAtoms() > 5:
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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25 mol.removeh()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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26 mol.OBMol.AddHydrogens(args.polar, True, args.pH)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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27 outfile.write(mol)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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28 outfile.close()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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29
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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30 def __main__():
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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31 """
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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32 Add hydrogen atoms at a certain pH value
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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33 """
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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34 args = parse_command_line(sys.argv)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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35 addh(args)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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37 if __name__ == "__main__" :
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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38 __main__()