Mercurial > repos > bgruening > openbabel_remduplicates
view remove_protonation_state.py @ 15:c5de6c19eb06 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author | bgruening |
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date | Thu, 15 Aug 2024 11:00:46 +0000 |
parents | 12aca74f07d7 |
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#!/usr/bin/env python """ Input: molecular input file. Output: Molecule file with removed ions and fragments. Copyright 2013, 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_protonation(args): outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) for mol in pybel.readfile(args.iformat, args.input): [atom.OBAtom.SetFormalCharge(0) for atom in mol.atoms] if "inchi" in mol.data: del mol.data["inchi"] # remove inchi cache so modified mol is saved outfile.write(mol) outfile.close() def __main__(): """ Remove any protonation state from each atom in each molecule. """ args = parse_command_line() remove_protonation(args) if __name__ == "__main__": __main__()