chembl_sim

ChEMBL Similarity Search

This code accompanies my blog post "What Do Molecules That Look LIke This Tend To Do"

Installation

This code requires the RDKit. For more information on installation set this link.

Install the necessary python libraries

pip install SQLAlchemy tqdm docopt
conda install -c conda-forge fpsim2

Download chembl_27_sqlite.tar.gz from ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/

wget ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_27_sqlite.tar.gz

Untar the file and put chembl_27.db somewhere and put the attached scripts in the same directory.

Create the fingerprint database, note that this takes a while

create_fpsim2_db.py chembl_27.db chembl_27.h5

Usage

Usage: chembl_sim.py --query QUERY_SMI --out OUT_CSV [--sim SIM_CUTOFF]

--help print this help message
--query QUERY_SMI query SMILES file (takes the form SMILES name)
--out OUT_CSV output csv file
--sim SIM_CUTOFF similarity cutoff, default=0.7

As an example:

chembl_sim_search.py --query query.smi --out out.csv

To set the similarity cutoff:

chembl_sim_search.py --query query.smi --out out.csv --sim 0.6

A More General Solution for Searching Databases Other Than ChEMBL

I also created a couple of scripts that will enable you to create and search FpSim2 databases from SMILES files. As a quick example

smi2fpsim2.py test.smi
search_fpsim2.py --query query.smi --db test --out test.csv --sim 0.3

Please see the help for these scripts for more information