Mercurial > repos > bgruening > ctb_remove_protonation_state

comparison ob_remIons.py @ 0:bdfd80d7586d 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 11:45:34 -0400
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-1:000000000000 0:bdfd80d7586d
1 #!/usr/bin/env python
2 """
3 Input: molecular input file.
4 Output: Molecule file with removed ions and fragments.
5 Copyright 2012, Bjoern Gruening and Xavier Lucas
6 """
7 import sys, os
8 import argparse
9 import openbabel
10 openbabel.obErrorLog.StopLogging()
11 import pybel
12
13 def parse_command_line():
14 parser = argparse.ArgumentParser()
15 parser.add_argument('-iformat', default='sdf' , help='input file format')
16 parser.add_argument('-i', '--input', required=True, help='input file name')
17 parser.add_argument('-o', '--output', required=True, help='output file name')
18 return parser.parse_args()
19
20 def remove_ions(args):
21 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
22 for mol in pybel.readfile(args.iformat, args.input):
23 if mol.OBMol.NumHvyAtoms() > 5:
24 mol.OBMol.StripSalts(0)
25 # Check if new small fragments have been created and remove them
26 if mol.OBMol.NumHvyAtoms() > 5:
27 outfile.write(mol)
28 outfile.close()
29
30 def __main__():
31 """
32 Remove any counterion and delete any fragment but the largest one for each molecule.
33 """
34 args = parse_command_line()
35 remove_ions(args)
36
37 if __name__ == "__main__" :
38 __main__()