# HG changeset patch # User bgruening # Date 1602323020 0 # Node ID 2f59c6239f256e8133fc597f0a08aff6d46c7641 "planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 78f2261af4e00c830ea311337d0aed9b297aad8e-dirty" diff -r 000000000000 -r 2f59c6239f25 chembl.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chembl.py Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,118 @@ +import argparse + +from chembl_webresource_client.new_client import new_client +from chembl_webresource_client.settings import Settings + +Settings.Instance().CACHING = False + + +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: + 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') + parser.add_argument('-f', '--file', help='SMILES input as file') + parser.add_argument('-o', '--output', help="SMILES output") + parser.add_argument('-t', '--tanimoto', type=int, help='Tanimoto similarity score') + parser.add_argument('-s', '--substructure', action='store_true', help='Substructure search using the SMILES input.') + parser.add_argument('-d', '--drugs', action='store_true', help='Filter approved drugs') + parser.add_argument('-b', '--biotherapeutic', action='store_true', help='Filter biotherapeutic molecules') + parser.add_argument('-n', '--nat-prod', action='store_true', help='Filter natural products') + parser.add_argument('-r', '--ro5', action='store_true', help='Filter compounds that pass Lipinski RO5') + + args = parser.parse_args() + + if args.file: # get SMILES from file rather than -i option + args.input = open_file(args.file) + + if len(args.input) < 5: + raise IOError('SMILES must be at least 5 characters long.') + + if args.substructure: # specify search type: substructure or similarity + mols = substr_search(args.input) + else: + mols = sim_search(args.input, args.tanimoto) + + # filter options: + if args.drugs: + mols = filter_drugs(mols) + + if args.biotherapeutic: + mols = filter_biotherapeutic(mols) + + if args.nat_prod: + mols = filter_nat_prod(mols) + + if args.ro5: + mols = filter_ro5(mols) + + # get SMILES from search output + mols = get_smiles(mols) + + # write to file + with open(args.output, 'w') as f: + f.write('\n'.join(mols)) + + +if __name__ == "__main__": + main() diff -r 000000000000 -r 2f59c6239f25 chembl_structure_pipeline.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chembl_structure_pipeline.xml Sat Oct 10 09:43:40 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 000000000000 -r 2f59c6239f25 structure_pipeline.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/structure_pipeline.py Sat Oct 10 09:43:40 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 000000000000 -r 2f59c6239f25 test-data/10mol.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10mol.sdf Sat Oct 10 09:43:40 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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0 0 2 0 0 0 + -4.1471 2.2892 0.0000 O 0 0 + -4.7748 1.2665 0.0000 C 0 0 + -0.9800 -0.7800 0.0000 N 0 0 + -2.1300 -1.4600 0.0000 C 0 0 + -3.3200 -0.7600 0.0000 C 0 0 + -4.5500 -1.4800 0.0000 C 0 0 + -4.5800 -2.7700 0.0000 C 0 0 + -3.3400 -3.4700 0.0000 C 0 0 + -2.1300 -2.7900 0.0000 C 0 0 + 0.2400 -2.7700 0.0000 C 0 0 + 1.4300 -3.4700 0.0000 C 0 0 + 1.7600 -4.9700 0.0000 C 0 0 + 3.2600 -5.0800 0.0000 N 0 0 + 3.8500 -3.6300 0.0000 C 0 0 + 4.9971 -3.2777 0.0000 O 0 0 + 2.6600 -2.7500 0.0000 C 0 0 + 2.6800 -1.4600 0.0000 C 0 0 + 3.7900 0.5600 0.0000 C 0 0 + 4.9600 1.2800 0.0000 C 0 0 + 4.9600 2.6300 0.0000 C 0 0 + 3.8100 3.2900 0.0000 C 0 0 + 2.6400 2.5900 0.0000 C 0 0 + 2.6400 1.2400 0.0000 C 0 0 + 1.4900 0.5400 0.0000 N 0 0 + 1.4500 -0.7600 0.0000 C 0 0 + 0.2400 -1.4400 0.0000 C 0 0 + 1 2 1 0 + 3 2 1 6 + 3 4 1 0 + 5 4 1 6 + 5 6 1 0 + 6 7 1 0 + 7 8 1 1 + 7 9 1 0 + 3 9 1 0 + 9 10 1 6 + 10 11 1 0 + 7 12 1 0 + 12 13 1 0 + 13 14 1 0 + 14 15 2 0 + 15 16 1 0 + 16 17 2 0 + 17 18 1 0 + 13 18 2 0 + 18 19 1 0 + 19 20 1 0 + 20 21 1 0 + 21 22 1 0 + 22 23 1 0 + 23 24 2 0 + 23 25 1 0 + 20 25 2 0 + 25 26 1 0 + 26 27 1 0 + 27 28 1 0 + 28 29 2 0 + 29 30 1 0 + 30 31 2 0 + 31 32 1 0 + 27 32 2 0 + 32 33 1 0 + 5 33 1 0 + 33 34 1 0 + 26 34 2 0 + 34 35 1 0 + 12 35 1 0 + 19 35 2 0 +M END +> +66 + +> +CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35 + +$$$$ + + SciTegic01171120562D + + 32 35 0 0 1 0 999 V2000 + 7.1381 -2.1568 0.0000 C 0 0 + 6.0456 -2.6531 0.0000 C 0 0 + 4.7409 -1.9129 0.0000 N 0 0 + 3.6552 -2.9294 0.0000 C 0 0 + 2.1855 -2.6254 0.0000 C 0 0 + 1.7138 -1.2033 0.0000 C 0 0 + 2.5889 0.0182 0.0000 C 0 0 + 3.7889 0.0269 0.0000 O 0 0 + 1.7138 1.2033 0.0000 N 0 0 + 0.2917 0.7475 0.0000 C 0 0 + -1.0028 1.5132 0.0000 C 0 0 + -2.3155 0.7475 0.0000 C 0 0 + -2.3155 -0.7475 0.0000 C 0 0 + -3.3560 -1.3452 0.0000 F 0 0 + -1.0028 -1.5132 0.0000 C 0 0 + 0.2917 -0.7475 0.0000 C 0 0 + 4.2542 -4.2907 0.0000 C 0 0 + 3.6559 -5.3308 0.0000 C 0 0 + 5.7448 -4.1226 0.0000 C 0 0 + 6.7580 -5.2264 0.0000 C 0 0 + 6.3978 -6.3710 0.0000 O 0 0 + 8.2231 -4.9012 0.0000 N 0 0 + 9.2380 -6.0068 0.0000 C 0 0 + 10.7032 -5.6816 0.0000 C 0 0 2 0 0 0 + 11.0634 -4.5369 0.0000 O 0 0 + 11.7181 -6.7872 0.0000 C 0 0 + 13.1833 -6.4620 0.0000 N 0 0 + 14.1993 -7.5656 0.0000 C 0 0 + 15.6630 -7.2376 0.0000 C 0 0 + 16.1108 -5.8060 0.0000 O 0 0 + 15.0949 -4.7024 0.0000 C 0 0 + 13.6312 -5.0304 0.0000 C 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 1 0 + 4 5 1 0 + 5 6 2 0 + 6 7 1 0 + 7 8 2 0 + 7 9 1 0 + 9 10 1 0 + 10 11 1 0 + 11 12 2 0 + 12 13 1 0 + 13 14 1 0 + 13 15 2 0 + 15 16 1 0 + 6 16 1 0 + 10 16 2 0 + 4 17 2 0 + 17 18 1 0 + 17 19 1 0 + 2 19 2 0 + 19 20 1 0 + 20 21 2 0 + 20 22 1 0 + 22 23 1 0 + 23 24 1 0 + 24 25 1 6 + 24 26 1 0 + 26 27 1 0 + 27 28 1 0 + 28 29 1 0 + 29 30 1 0 + 30 31 1 0 + 31 32 1 0 + 27 32 1 0 +M END +> +4362206 + +> +Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4 + +$$$$ diff -r 000000000000 -r 2f59c6239f25 test-data/check.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/check.mol Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,17 @@ + +Mrv1810 07121910172D + + 4 3 0 0 0 0 999 V2000 + -2.5038 0.4060 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + -2.5038 1.2310 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -3.2182 -0.0065 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 + -1.7893 -0.0065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 3 1 0 0 0 0 + 1 4 1 4 0 0 0 +M CHG 2 2 -1 3 1 +M END +> +5 +> +molecule has a bond with an illegal stereo flag; InChI: Proton(s) added/removed; InChI: Omitted undefined stereo \ No newline at end of file diff -r 000000000000 -r 2f59c6239f25 test-data/in1.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in1.smi Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,1 @@ +CN1CCC[C@H]1c2cccnc2 test diff -r 000000000000 -r 2f59c6239f25 test-data/o_molblock.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/o_molblock.mol Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,13 @@ + + Mrv1810 07121910172D + + 4 3 0 0 0 0 999 V2000 + -2.5038 0.4060 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + -2.5038 1.2310 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + -3.2182 -0.0065 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 + -1.7893 -0.0065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 3 1 0 0 0 0 + 1 4 1 4 0 0 0 +M CHG 2 2 -1 3 1 +M END diff -r 000000000000 -r 2f59c6239f25 test-data/out1.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out1.smi Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,47 @@ +CN1CCCC1c2ccc(Cl)cc2 CHEMBL279352 +CCCC[C@H]1CC[C@H](N1C)c2cccnc2 CHEMBL119581 +CN1CCCC1c2ccc(F)nc2 CHEMBL72470 +C[C@H]1CC[C@H](N1C)c2cccnc2 CHEMBL116645 +CCCC[C@@H]1CC[C@H](N1C)c2cccnc2 CHEMBL119574 +CN1CCCC1c2ccc(CCc3ccc(Cl)cc3)nc2 CHEMBL189470 +CN1CCC[C@H]1c2cccnc2 CHEMBL3 +CN1CCCC1c2cncc(Cl)c2 CHEMBL61013 +CCCCCc1ccc(cn1)C2CCCN2C CHEMBL103566 +CN1CCCC1c2cccnc2 CHEMBL440464 +CN1CCCC1c2ccc(nc2)c3ccccc3 CHEMBL350748 +CN1CCCC1c2cnccc2N CHEMBL193763 +C(N1CCCC1c2cccnc2)c3ccccc3 CHEMBL163552 +COCC1CCN(C)[C@@H]1c2cccnc2 CHEMBL119020 +CN1CCCC1c2ccc(C)nc2 CHEMBL294757 +CN1CCCC1c2ccc(C)cc2 CHEMBL180376 +CN1CCCC[C@H]1c2cccnc2 CHEMBL3640783 +C[C@@H]1CC[C@H](N1C)c2cccnc2 CHEMBL118038 +CN1CCC[C@H]1c2ccccn2 CHEMBL2068760 +CN1CCCC1c2cccnc2C CHEMBL160034 +CCc1ccc(cn1)C2CCCN2C CHEMBL103225 +C[C@H]1C[C@H](N(C)C1)c2cccnc2 CHEMBL432837 +CC[C@H]1C[C@H](N(C)C1)c2cccnc2 CHEMBL115793 +CN1CCCC1c2ccccc2 CHEMBL367126 +CN1CCCC1c2ccc(CCCc3ccccc3)nc2 CHEMBL361703 +CC1CCN(C)[C@@H]1c2cccnc2 CHEMBL119019 +CN1CCCC1c2ccc(Br)nc2 CHEMBL58231 +CN1CCCCC1c2cccnc2 CHEMBL102246 +CN1CCCC1c2ccc(CCc3ccccc3)nc2 CHEMBL190295 +CN1CCC[C@H]1c2ccccc2 CHEMBL1199383 +COc1cncc(c1)C2CCCN2C CHEMBL303530 +COc1ccc(CCc2ccc(cn2)C3CCCN3C)cc1 CHEMBL190652 +CN1CCCC1c2cncc(F)c2 CHEMBL62128 +CN1CCCC1c2cncc(C)c2 CHEMBL364003 +CN1CCC(CO)[C@H]1c2cccnc2 CHEMBL325426 +CCN1CCCC1c2cccnc2 CHEMBL163042 +COc1ccncc1C2CCCN2C CHEMBL370168 +CCc1cncc(c1)C2CCCN2C CHEMBL111526 +CN1CCC[C@@H]1c2cccnc2 CHEMBL9732 +CN1CCC(CF)[C@H]1c2cccnc2 CHEMBL119016 +CN1CCCC1c2ccc(Cl)nc2 CHEMBL70050 +CN1CCCC1c2cncc(Br)c2 CHEMBL61772 +CN1CCCC1c2ccc(\C=C\c3ccccc3)nc2 CHEMBL190678 +CCCc1cncc(c1)C2CCCN2C CHEMBL382287 +CN1CCCC1c2cnc3ccccc3c2 CHEMBL161944 +CCCc1ccc(cn1)C2CCCN2C CHEMBL103537 +CCCCc1ccc(cn1)C2CCCN2C CHEMBL320023 \ No newline at end of file diff -r 000000000000 -r 2f59c6239f25 test-data/out2.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out2.smi Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,1 @@ +CN1CCC[C@H]1c2cccnc2 CHEMBL3 \ No newline at end of file diff -r 000000000000 -r 2f59c6239f25 test-data/out3.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out3.smi Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,55 @@ +CN1CCC[C@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O CHEMBL1448280 +Cn1cccc1-c1cc(C(=O)N2CCCC2c2cccnc2)[nH]n1 CHEMBL3486928 +O=C1[C@@H](NS(=O)(=O)c2ccc3cc(Cl)ccc3c2)CCCN1CC(=O)N1CCCC1c1cccnc1 CHEMBL1923459 +CN1CCCC1c1cccnc1.O=S(=O)(O)O CHEMBL2142095 +CN1CCC[C@@H]1c1cccnc1.Cc1ccc(C(=O)OC(C(=O)O)C(OC(=O)c2ccc(C)cc2)C(=O)O)cc1 CHEMBL2448607 +NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)c2ccccc12 CHEMBL4095563 +O=C(NC1CCN(Cc2ccn(-c3ccc(C(F)(F)F)cc3)c2)CC1)N1CCCC1c1cccnc1 CHEMBL560283 +O=C1NC(=O)/C(=C/c2cnn3c(NC4CC4)nc(N4CCCC4c4cccnc4)nc23)N1 CHEMBL3984229 +O=S(=O)(Nc1ncns1)c1ccc2c(N3CCC[C@H]3c3cccnc3)cccc2c1 CHEMBL3692144 +O=C(c1cc2c([nH]c1=O)CCC2)N1CCCC1c1cccnc1 CHEMBL3458802 +CC(C)C[C@H](N[C@H](CCN1C(=O)c2cc3ccccc3cc2C1=O)C(=O)O)C(=O)N1CCCC1c1cccnc1 CHEMBL158622 +c1ccc(CN2CCCC2c2cccnc2)cc1 CHEMBL163552 +Cc1ncsc1CCC(=O)N1CCCC1c1cccnc1 CHEMBL3476252 +O=C(c1cc(-c2ccc(O)cc2)n[nH]1)N1CCCC1c1cccnc1 CHEMBL3474057 +O=C(C(Nc1ccccc1F)c1cc2ccccc2s1)N1CCCC1c1cccnc1 CHEMBL2348659 +OC(COc1ccccc1-c1nc2ccccc2o1)CN1CCCC1c1cccnc1 CHEMBL608832 +O=C(Nc1ccccc1F)N1CCCC1c1cccnc1 CHEMBL1870182 +CN1CCC[C@H]1c1cccnc1.Cl CHEMBL225057 +O=C(Nc1ccccc1C(F)(F)F)N1CCCC1c1cccnc1 CHEMBL1353542 +CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H](C[C@H](O)[C@@]21C)[C@@]1(C)CC[C@@H](O)C[C@H]1C[C@H]3O CHEMBL3114538 +Cc1ccc2nc(CN3CCCC3c3cccnc3)cc(O)c2c1 CHEMBL3485916 +Cc1cc(N2CCCC2c2cccnc2)nc(C)n1 CHEMBL3454373 +O=S(=O)(Nc1ncns1)c1ccc2c(N3CCC[C@@H]3c3cccnc3)cccc2c1 CHEMBL3682682 +CN1CCCC1c1cccnc1 CHEMBL440464 +CN1CCC[C@@H]1c1cccnc1 CHEMBL9732 +Cc1cc(N(C)C)nc(N2CCCC2c2cccnc2)n1 CHEMBL3454403 +CN1CCC[C@H]1c1cccnc1.CN1CCC[C@H]1c1cccnc1.O=S(=O)(O)O CHEMBL3182465 +CCCc1cc(C(=O)N2CCCC2c2cccnc2)[nH]n1 CHEMBL3486295 +O=C(c1ccc(F)c(F)c1)N1CCN2C(=O)c3ccccc3[C@@]12c1ccc(N2CCC[C@H]2c2cccnc2)cc1 CHEMBL4100810 +CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@@]21C CHEMBL3114539 +CCNC(=O)c1cc2c(N3CCCC3c3cccnc3)ccnc2[nH]1 CHEMBL4064004 +Cc1nn(C)c(Oc2cccc(Cl)c2Cl)c1C(=O)N1CCCC1c1cccnc1 CHEMBL2336227 +CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@@]21C CHEMBL3114541 +CC1=C(C(=O)N2CCCC2c2cccnc2)C(c2ccc(Cl)c(Cl)c2)n2nccc2N1 CHEMBL601248 +NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)nc1 CHEMBL1921840 +c1cncc(C2CCCN2c2ccnc3[nH]ncc23)c1 CHEMBL4066892 +CN1CCC[C@H]1c1cccnc1 CHEMBL3 +CCO.CN1CCC[C@H]1c1cccnc1 CHEMBL3137669 +Cc1cc(C)nc(N2CCCC2c2cccnc2)n1 CHEMBL3436596 +Cc1ccc(-c2cc(C(=O)N3CCCC3c3cccnc3)[nH]n2)o1 CHEMBL3485246 +NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)c(Cl)c1 CHEMBL1921841 +NC(=O)c1ccc(Oc2ccc(CN3CCC[C@@H]3c3cccnc3)cc2)c(Cl)c1 CHEMBL1921843 +NC(=O)c1ccc(Oc2ccc(CN3CCC[C@H]3c3cccnc3)cc2)c(Cl)c1 CHEMBL1921842 +CN1CCC[C@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O CHEMBL151515 +O=C(C(Nc1ccccc1F)c1ccc(C(F)(F)F)cc1)N1CCCC1c1cccnc1 CHEMBL2348671 +CN1CCC[C@H]1c1cccnc1.O.O.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O CHEMBL3989563 +c1cncc(C2CCCN2C2c3ccccc3Oc3ccccc32)c1 CHEMBL278775 +CN1CCC[C@@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O CHEMBL2062338 +Cn1cc(NC(=O)N2CCCC2c2cccnc2)ccc1=O CHEMBL3453894 +CCN1CCCC1c1cccnc1 CHEMBL163042 +O=S(=O)(Nc1ncns1)c1ccc2c(N3CCCC3c3cccnc3)cccc2c1 CHEMBL3682681 +O=C(NC1COC1)c1cc2c(N3CCCC3c3cccnc3)ccnc2[nH]1 CHEMBL4083992 +O=CN1CCC[C@H]1c1cccnc1 CHEMBL3126024 +Cc1nc2ccccc2n1Cc1ccc(CNC(=O)[C@H](O)[C@@H](O)C(=O)N2CCCC2c2cccnc2)s1 CHEMBL1779603 +CC[C@H]1OC(=O)[C@H](C)[C@@H](OC(=O)N2CCC[C@@H]2c2cccnc2)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@H](N(C)C)[C@H]2O)[C@](C)(OC)C[C@@H](C)C(=O)[C@H](C)[C@H]2NC(=O)O[C@]12C CHEMBL2338711 \ No newline at end of file diff -r 000000000000 -r 2f59c6239f25 test-data/out4.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out4.smi Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,4 @@ +C1CCCC1 CHEMBL1370850 +C1CCCCCCCCCCC1 CHEMBL3185808 +C1CCCCCCC1 CHEMBL452651 +C1CCCCC1 CHEMBL15980 \ No newline at end of file diff -r 000000000000 -r 2f59c6239f25 test-data/parent_molblock.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/parent_molblock.mol Sat Oct 10 09:43:40 2020 +0000 @@ -0,0 +1,12 @@ + + RDKit 2D + + 4 3 0 0 0 0 0 0 0 0999 V2000 + -2.5038 0.4060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5038 1.2310 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2182 -0.0065 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7893 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