Mercurial > repos > bgruening > openbabel_spectrophore_search
view ob_remIons.py @ 13:9ce9f996b941 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author | bgruening |
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date | Mon, 19 Oct 2020 14:41:00 +0000 |
parents | afd14e10a318 |
children | 330514267c57 |
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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 argparse from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() 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) if 'inchi' in mol.data: del mol.data['inchi'] # remove inchi cache so modified mol is saved # 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__()