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annotate ob_addh.py @ 0:631cd009009b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
author bgruening
date Tue, 31 May 2016 11:46:16 -0400
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631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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1 #!/usr/bin/env python
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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2 """
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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3 Input: Molecule file
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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4 Output: Molecule file with hydrogen atoms added at the target pH.
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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5 """
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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6 import sys, os
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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7 import argparse
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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8 import openbabel
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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9 openbabel.obErrorLog.StopLogging()
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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10 import pybel
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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11
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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12 def parse_command_line(argv):
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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13 parser = argparse.ArgumentParser()
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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14 parser.add_argument('--iformat', type=str, default='sdf' , help='input file format')
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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15 parser.add_argument('-i', '--input', type=str, required=True, help='input file name')
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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16 parser.add_argument('-o', '--output', type=str, required=True, help='output file name')
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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17 parser.add_argument('--polar', action="store_true", default=False, help='Add hydrogen atoms only to polar atoms')
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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18 parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value')
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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19 return parser.parse_args()
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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21 def addh(args):
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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22 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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23 for mol in pybel.readfile(args.iformat, args.input):
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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24 if mol.OBMol.NumHvyAtoms() > 5:
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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25 mol.removeh()
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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26 mol.OBMol.AddHydrogens(args.polar, True, args.pH)
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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27 outfile.write(mol)
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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28 outfile.close()
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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30 def __main__():
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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31 """
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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32 Add hydrogen atoms at a certain pH value
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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33 """
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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34 args = parse_command_line(sys.argv)
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
bgruening
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35 addh(args)
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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37 if __name__ == "__main__" :
631cd009009b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 4a60df09ddf9dfcedad80f7b72a927198da2f755
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38 __main__()