Mercurial > repos > bgruening > _obgrep
comparison ob_remIons.py @ 0:8d51a2cee5c0 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 08:38:55 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:8d51a2cee5c0 |
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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 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__() |