Mercurial > repos > bgruening > openbabel_obgrep

comparison remove_protonation_state.py @ 0:b0311f002a5f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
author bgruening
date Sat, 20 May 2017 08:59:45 -0400
parents
children 78640d0127ce
comparison
equal deleted inserted replaced
-1:000000000000 0:b0311f002a5f
1 #!/usr/bin/env python
2 """
3 Input: molecular input file.
4 Output: Molecule file with removed ions and fragments.
5 Copyright 2013, 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_protonation( args ):
21 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
22 for mol in pybel.readfile(args.iformat, args.input):
23 [atom.OBAtom.SetFormalCharge(0) for atom in mol.atoms]
24 outfile.write( mol )
25 outfile.close()
26
27 def __main__():
28 """
29 Remove any protonation state from each atom in each molecule.
30 """
31 args = parse_command_line()
32 remove_protonation( args )
33
34 if __name__ == "__main__" :
35 __main__()