MongoDB Chemistry

Chemical similarity search implementation in MongoDB, with performance analysis.

See this blog post for more information.

See also:

• Presentation slides
• Blog post by Rajarshi Guha
• Blog post by Davy Suvee (part 2, part 3)

Installation

Mac OS X

brew install rdkit mongodb
pip install git+https://github.com/mcs07/mongodb-chemistry.git

Ubuntu

See scripts/bootstrap.sh.

Usage

A simple example:

mchem load mymols.sdf
mchem addfp
mchem countfp
mchem similar O=C(Oc1ccccc1C(=O)O)C

See scripts/chembl.sh for a more detailed example.