/chembl_tools

Small scripts to make the most of the ChEMBL API

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

chembl_tools

A series of scripts to make the most of the ChEMBL API

prerequisites

  • python 2.7+, 3.3+
  • chembl_webresource_client

example

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

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 <marco@ebi.ac.uk>.

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/>.