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
This program is free software: you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation, either version 3 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
Neither the institution name nor the name chembl_tools
can be used to endorse or promote products derived from
this software without prior written permission.
For written permission, please contact <[email protected]>.
Products derived from this software may not be called chembl_tools
nor may chembl_tools appear in their names without prior written
permission of the developers. You should have received a copy
of the GNU General Public License along with this program.
If not, see <http://www.gnu.org/licenses/>.