Mercurial > repos > bgruening > openbabel_remsmall
view ob_remIons.py @ 2:ab4318b816bd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 78ac0521d7df684e96c1b9c1ba2a17b02e681608
author | bgruening |
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date | Sat, 20 May 2017 20:04:20 -0400 |
parents | 2704d4017b13 |
children | aebc671bae78 |
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#!/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__()