Mercurial > repos > bgruening > openbabel_addh
comparison remove_protonation_state.py @ 0:ada6daa717d2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 08:37:26 -0400 |
| parents | |
| children | 43167f164076 |
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| -1:000000000000 | 0:ada6daa717d2 |
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| 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__() |