Mercurial > repos > bgruening > openbabel_svg_depiction
view ob_addh.py @ 13:a66827fc370d 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 14:45:37 +0000 |
parents | d3b48303045b |
children | 75ee9c410951 |
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#!/usr/bin/env python """ Input: Molecule file Output: Molecule file with hydrogen atoms added at the target pH. """ import argparse import sys from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() def parse_command_line(argv): parser = argparse.ArgumentParser() parser.add_argument('--iformat', type=str, default='sdf', help='input file format') parser.add_argument('-i', '--input', type=str, required=True, help='input file name') parser.add_argument('-o', '--output', type=str, required=True, help='output file name') parser.add_argument('--polar', action="store_true", default=False, help='Add hydrogen atoms only to polar atoms') parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value') return parser.parse_args() def addh(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.removeh() mol.OBMol.AddHydrogens(args.polar, True, args.pH) outfile.write(mol) outfile.close() def __main__(): """ Add hydrogen atoms at a certain pH value """ args = parse_command_line(sys.argv) addh(args) if __name__ == "__main__": __main__()