About ChemFP

chemfp makes cheminformatics fingerprints easy and fast.


With chemfp, you get command-line programs for fingerprint generation and high-performance similarity search. The tools support the FPS fingerprint file format, so if you want something beyond the OEChem, Open Babel and RDKit fingerprinters then you can write your own FPS files and still use the fast Tanimoto search tool. The programs are written in Python, with a C extension for better performance. The core Python module is documented, which means you can write your own programs on top of the core API.

Licensing options

The commercial license is available for €22 000 (+VAT in the EU). It includes access to chemfp-1.2, free upgrades for one year, support, and reduced rates for support contract renewal.

The goal with version 1.2 is to make web development easy, across all of the supported toolkits. Some of the new features include:

  • binary FPB format support for fast load times, with 0.1 second searches from the command-line!
  • support for reading structures from a string, in addition to a file
  • new APIs to discover the available fingerprint types
  • new toolkit API molecule I/O, tied to each fingerprint type so your code can easily use the most
No-cost version

Version 1.1 of the chemfp toolkit is available at no cost under the MIT/BSD license. New features will be added to the commercial version first, and the no-cost version will eventually lag by about three years.