Mercurial > repos > bgruening > chembl
view structure_pipeline.py @ 7:1d6fb7967ae9 draft
"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 78f2261af4e00c830ea311337d0aed9b297aad8e-dirty"
author | bgruening |
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date | Sat, 10 Oct 2020 09:43:14 +0000 |
parents | a57de37f12c2 |
children |
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import argparse from chembl_structure_pipeline import checker, standardizer def load_mols(input_file): """ Returns a list of strings, each a molblock """ with open(input_file) as f: mols = [''.join(('\n', mol.strip())) for mol in f.read().strip().split('$$$$\n')] return mols def write_mols(mols, output_file): """ Writes a list of molblocks to an SDF """ with open(output_file, 'w') as f: f.write('\n$$$$'.join(mols)) def standardize_molblock(mol): return standardizer.standardize_molblock(mol) def get_parent_molblock(mol): return standardizer.get_parent_molblock(mol)[0] def check_molblock(mol): issues = checker.check_molblock(mol) max_penalty_score = str(max([issue[0] for issue in issues])) if issues else '0' message = '; '.join([issue[1] for issue in issues]) mol_with_issues = '\n'.join((mol, '> <MaxPenaltyScore>', max_penalty_score, '> <IssueMessages>', message)) return mol_with_issues def main(): parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds') parser.add_argument('-i', '--input', help='SDF/MOL input') parser.add_argument('-o', '--output', help="Standardized output") parser.add_argument('--standardize', action='store_true', help="Standardize molblock") parser.add_argument('--get_parent', action='store_true', help="Get parent molblock.") parser.add_argument('--check', action='store_true', help="Check molblock") args = parser.parse_args() mols = load_mols(args.input) if args.standardize: mols = [standardize_molblock(mol) for mol in mols] if args.get_parent: mols = [get_parent_molblock(mol) for mol in mols] if args.check: mols = [check_molblock(mol) for mol in mols] write_mols(mols, args.output) if __name__ == "__main__": main()