# HG changeset patch # User bgruening # Date 1602063100 0 # Node ID a57de37f12c239ca496c6b3f2df464a792e9deb2 # Parent 1ade252ebe081cf42e35a3c9f168bb5ca37d2b38 "planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 78f2261af4e00c830ea311337d0aed9b297aad8e" diff -r 1ade252ebe08 -r a57de37f12c2 chembl.py --- a/chembl.py Tue Jul 28 08:20:47 2020 -0400 +++ b/chembl.py Wed Oct 07 09:31:40 2020 +0000 @@ -1,62 +1,73 @@ +import argparse + +from chembl_webresource_client.new_client import new_client from chembl_webresource_client.settings import Settings + Settings.Instance().CACHING = False -from chembl_webresource_client.new_client import new_client -import argparse + def open_file(filename): with open(filename) as f: return f.readline().split()[0] + def get_smiles(res): """ Get a list of SMILES from function results - """ + """ smiles = set() - for smi in res: + for smi in res: try: smiles.add('{}\t{}'.format(smi['molecule_structures']['canonical_smiles'], smi['molecule_chembl_id'])) except TypeError: continue return smiles + def sim_search(smiles, tanimoto): """ Return compounds which are within a Tanimoto range of the SMILES input """ similarity = new_client.similarity return similarity.filter(smiles=smiles, similarity=tanimoto).only(['molecule_structures', 'molecule_chembl_id']) - + + def substr_search(smiles): """ Return compounds which contain the SMILES substructure input """ substructure = new_client.substructure return substructure.filter(smiles=smiles).only(['molecule_structures', 'molecule_chembl_id']) - + + def filter_drugs(mols): """ Return only compounds which are approved drugs """ return mols.filter(max_phase=4) + def filter_biotherapeutic(mols): """ Return only biotherapeutic molecules """ return mols.filter(biotherapeutic__isnull=False) + def filter_nat_prod(mols): """ Return only natural products """ return mols.filter(natural_product=1) + def filter_ro5(mols): """ Return only compounds with no RO5 violations """ return mols.filter(molecule_properties__num_ro5_violations=0) + def main(): parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds') parser.add_argument('-i', '--input', help='SMILES input') @@ -101,7 +112,7 @@ # write to file with open(args.output, 'w') as f: f.write('\n'.join(mols)) - + if __name__ == "__main__": main() diff -r 1ade252ebe08 -r a57de37f12c2 chembl.xml --- a/chembl.xml Tue Jul 28 08:20:47 2020 -0400 +++ b/chembl.xml Wed Oct 07 09:31:40 2020 +0000 @@ -1,9 +1,9 @@ + for compounds which are similar to a SMILES string 0.10.1 2 - for compounds which are similar to a SMILES string chembl_webresource_client diff -r 1ade252ebe08 -r a57de37f12c2 chembl_structure_pipeline.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chembl_structure_pipeline.xml Wed Oct 07 09:31:40 2020 +0000 @@ -0,0 +1,85 @@ + + for curation and standardizing of molecular structures + + 1.0.0 + 0 + + + chembl_structure_pipeline + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `. A list of all errors encountered is recorded under ``. + +Either one or more of these protocols can be applied in a single Galaxy job. + +----- + +.. class:: infomark + +**Input** + +One or more molecules in MOL/SDF format. + +----- + +.. class:: infomark + +**Output** + +A MOL/SD-file containing the processed molecules. + +]]> + + 10.1186/s13321-020-00456-1 + + diff -r 1ade252ebe08 -r a57de37f12c2 structure_pipeline.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/structure_pipeline.py Wed Oct 07 09:31:40 2020 +0000 @@ -0,0 +1,59 @@ +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, '> ', max_penalty_score, '> ', 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() diff -r 1ade252ebe08 -r a57de37f12c2 test-data/10mol.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10mol.sdf Wed Oct 07 09:31:40 2020 +0000 @@ -0,0 +1,759 @@ + + SciTegic01171120562D + + 26 30 0 0 0 0 999 V2000 + -8.6396 0.9568 0.0000 O 0 0 + -7.6023 1.5602 0.0000 C 0 0 + -7.6071 3.0602 0.0000 C 0 0 + -6.3104 3.8143 0.0000 C 0 0 + -5.0090 3.0685 0.0000 C 0 0 + -5.0040 1.5682 0.0000 C 0 0 + -6.3008 0.8143 0.0000 C 0 0 + -3.7006 0.8244 0.0000 C 0 0 + -3.7006 -0.6045 0.0000 N 0 0 + -2.4915 -1.3190 0.0000 C 0 0 + -2.5059 -2.8197 0.0000 N 0 0 + -1.2156 -3.5847 0.0000 C 0 0 + -1.2329 -5.0846 0.0000 C 0 0 + -2.5404 -5.8196 0.0000 O 0 0 + -3.8308 -5.0547 0.0000 C 0 0 + 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