Mercurial > repos > bgruening > prepare_ligands_for_docking
diff ob_addh.py @ 5:a5f4b80e6769 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
| author | bgruening |
|---|---|
| date | Mon, 19 Oct 2020 14:48:46 +0000 |
| parents | de4c80d17527 |
| children | fac2c28b4c55 |
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--- a/ob_addh.py Tue Jul 28 08:40:43 2020 -0400 +++ b/ob_addh.py Mon Oct 19 14:48:46 2020 +0000 @@ -3,21 +3,23 @@ Input: Molecule file Output: Molecule file with hydrogen atoms added at the target pH. """ -import sys, os 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('--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): @@ -27,6 +29,7 @@ outfile.write(mol) outfile.close() + def __main__(): """ Add hydrogen atoms at a certain pH value @@ -34,5 +37,6 @@ args = parse_command_line(sys.argv) addh(args) -if __name__ == "__main__" : + +if __name__ == "__main__": __main__()