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