Mercurial > repos > bgruening > openbabel_remduplicates
view ob_remIons.py @ 14:b2569e22b40c draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author | bgruening |
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date | Tue, 10 Nov 2020 20:30:47 +0000 |
parents | 12aca74f07d7 |
children | c5de6c19eb06 |
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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') 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__()