A series of scripts to make the most of the ChEMBL API
- python 2.7+, 3.3+
- chembl_webresource_client
Given a list of compound names, for instance:
amoxicillin
oxacillin
amikacin
rifampicin
garbage
pseudomonic acid
We first retrieve the corresponding ChEMBL IDs:
>>> src/get_chembl_ids compounds.txt > compounds.tsv
Found no exact match for "garbage", trying a search
Found no match for "garbage", skipping
Found no exact match for "pseudomonic acid", trying a search
We can then retrieve the Uniprot IDs for the targets of each compound in a predefined species:
>>> src/get_target_ids compounds.tsv --organism "Escherichia coli"
chembl target
CHEMBL1082 Q8GDC1
CHEMBL1082 P00959
CHEMBL1082 P62593
CHEMBL1082 P00811
CHEMBL1082 P0AD63
CHEMBL1082 A5HJU3
CHEMBL1082 Q5U7L7
CHEMBL177 P0A9A6
CHEMBL374478 P0A8V2
Or retrieve similar molecules with a predefined similarity threshold:
>>> src/get_similar_molecules compounds.tsv --similarity 99
query target
CHEMBL177 CHEMBL3637935
CHEMBL177 CHEMBL3348834
CHEMBL177 CHEMBL1625316
CHEMBL177 CHEMBL1625035
CHEMBL1082 CHEMBL1433952
CHEMBL1082 CHEMBL1367635
CHEMBL1082 CHEMBL1473908
CHEMBL1082 CHEMBL174
CHEMBL819 CHEMBL3558540
Copyright (C) <2017> EMBL-European Bioinformatics Institute
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