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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 2012, Bjoern Gruening and Xavier Lucas
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6 """
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7 import sys, os
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8 import argparse
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9 import openbabel
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10 openbabel.obErrorLog.StopLogging()
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11 import pybel
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12
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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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19
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20 def remove_ions(args):
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21 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
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22 for mol in pybel.readfile(args.iformat, args.input):
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23 if mol.OBMol.NumHvyAtoms() > 5:
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24 mol.OBMol.StripSalts(0)
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25 # Check if new small fragments have been created and remove them
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26 if mol.OBMol.NumHvyAtoms() > 5:
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27 outfile.write(mol)
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28 outfile.close()
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29
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30 def __main__():
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31 """
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32 Remove any counterion and delete any fragment but the largest one for each molecule.
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33 """
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34 args = parse_command_line()
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35 remove_ions(args)
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36
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37 if __name__ == "__main__" :
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38 __main__()
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