Mercurial > repos > bgruening > openbabel_remove_protonation_state
view ob_remIons.py @ 15:22a866858b81 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author | bgruening |
---|---|
date | Thu, 15 Aug 2024 11:00:20 +0000 |
parents | e376ba0fcde0 |
children |
line wrap: on
line source
#!/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") parser.add_argument( "-idx", default=False, action="store_true", help="should output be an indexed text table? works only for inchi/smiles, otherwise is ignored", ) return parser.parse_args() def remove_ions(args): with open(args.output, "w") as outfile: for index, mol in enumerate(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 mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else "\n" if args.idx and args.iformat in ["inchi", "smi"]: outfile.write(f"{index}\t{mol}") elif mol != "\n": outfile.write(f"{mol}") 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__()