Mercurial > repos > bgruening > openbabel_obgrep
diff ob_remIons.py @ 0:b0311f002a5f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
author | bgruening |
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date | Sat, 20 May 2017 08:59:45 -0400 |
parents | |
children | 78640d0127ce |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ob_remIons.py Sat May 20 08:59:45 2017 -0400 @@ -0,0 +1,38 @@ +#!/usr/bin/env python +""" + Input: molecular input file. + Output: Molecule file with removed ions and fragments. + Copyright 2012, Bjoern Gruening and Xavier Lucas +""" +import sys, os +import argparse +import openbabel +openbabel.obErrorLog.StopLogging() +import pybel + +def parse_command_line(): + parser = argparse.ArgumentParser() + parser.add_argument('-iformat', default='sdf' , help='input file format') + parser.add_argument('-i', '--input', required=True, help='input file name') + parser.add_argument('-o', '--output', required=True, help='output file name') + return parser.parse_args() + +def remove_ions(args): + outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) + for mol in pybel.readfile(args.iformat, args.input): + if mol.OBMol.NumHvyAtoms() > 5: + mol.OBMol.StripSalts(0) + # Check if new small fragments have been created and remove them + if mol.OBMol.NumHvyAtoms() > 5: + outfile.write(mol) + outfile.close() + +def __main__(): + """ + Remove any counterion and delete any fragment but the largest one for each molecule. + """ + args = parse_command_line() + remove_ions(args) + +if __name__ == "__main__" : + __main__()