chemfp is a set of tools and a Python API for working with cheminformatics fingerprints.

It can generate fingerprints using OEChem/OEGraphSim, Open Babel, and RDKit. It can also extract fingerprints from tags in an SD file. Most people use it for its high-performance Tanimoto and Tversky similarity search algorithms.

All versions of chemfp are distributed under the MIT license. (It contains some third-party components which are under equally permissive licenses, like the BSD or Python licenses.)

In addition, versions 1.0 and 1.1 were available at no cost.

Version 2.0 was the first release as commercial open source software. Customers needed to pay me for access to the software, which they received under the MIT license. The goal was to provide a revenue stream so I could continue to develop chemfp.

I now maintain two versions of chemfp. The 1.x line contines to be available at no cost, and the 3.x line is commercial open source.

Chemfp development uses a private repository, for obvious reasons. I use Read The Docs to view the documentation, but Read The Docs needs access to a public repository.

My solution is to export the documentation from chemfp into the chemfp_documentation repository.

For more information on chemfp, either read the documentation or go to


Last Built

3 days, 20 hours ago passed


Home Page



cheminformatics, chemoinformatics, Tanimoto, fingerprint similarity

Project Privacy Level


Short URLs

Default Version


'latest' Version