Mercurial > repos > bgruening > openbabel_obgrep

annotate ob_remIons.py @ 3:95ad9ec29ad4 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c84729ec58f7f52d594066158afed175208d3d66
author bgruening
date Wed, 24 May 2017 09:59:42 -0400
parents b7797c0e2ec9
children 701b8995f6d1
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b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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1 #!/usr/bin/env python
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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2 """
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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3 Input: molecular input file.
b7797c0e2ec9 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 removed ions and fragments.
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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5 Copyright 2012, Bjoern Gruening and Xavier Lucas
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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6 """
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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7 import sys, os
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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8 import argparse
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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9 import openbabel
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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10 openbabel.obErrorLog.StopLogging()
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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11 import pybel
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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12
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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13 def parse_command_line():
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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14 parser = argparse.ArgumentParser()
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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15 parser.add_argument('-iformat', default='sdf' , help='input file format')
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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16 parser.add_argument('-i', '--input', required=True, help='input file name')
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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17 parser.add_argument('-o', '--output', required=True, help='output file name')
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
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18 return parser.parse_args()
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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20 def remove_ions(args):
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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21 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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22 for mol in pybel.readfile(args.iformat, args.input):
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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23 if mol.OBMol.NumHvyAtoms() > 5:
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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24 mol.OBMol.StripSalts(0)
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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25 # Check if new small fragments have been created and remove them
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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26 if mol.OBMol.NumHvyAtoms() > 5:
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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27 outfile.write(mol)
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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28 outfile.close()
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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30 def __main__():
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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31 """
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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32 Remove any counterion and delete any fragment but the largest one for each molecule.
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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33 """
b7797c0e2ec9 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()
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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35 remove_ions(args)
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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37 if __name__ == "__main__" :
b7797c0e2ec9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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38 __main__()