Suite of tools for indexing and searching similar molecules in Elasticsearch

Tool for finding chemical molecules, compounds, reactions, etc in PubChem (https://pubchem.ncbi.nlm.nih.gov/)

Index pubchem dump into Elasticsearch

docker-compose -f elastic/docker-compose.yml up 
cd pubchem/
export PYTHONPATH=$(pwd)
python3 pubchem.py pull

By default pubchem uses pubchem/ folder in your home directory. You can change this directory using --workdir flag.

--tmpdir should be pointed to SSD. If you already use ssd for --workdir, you can skip this option.

Molecule similarity in Elasticsearch