Chemfp is a set of command-line tools and a Python library for working with cheminformatics fingerprints. It can use OEChem/OEGraphSim, RDKit, or Open Babel to create fingerprints in the FPS format, and it implements a high-speed Tanimoto search.

The software is available under the MIT license. For more information see http://chemfp.com/. Documentation is available from http://chemfp.readthedocs.io/en/chemfp-1.3/ .

There are many changes over chemfp 1.1, which was the last release of the public/no-cost version of chemfp. The biggest ones are:

• Tested against the current version of all of the toolkits

• Added support for the Avalon and pattern fingerprints in RDKit

• In-memory Tanimoto searches for 166-bit MACCS keys on computers with the POPCNT instruction is about 30% faster.

• FPS loading is about 40% faster. As a result, file-based searches are about 25% faster.

• The in-memory search algorithms in version 1.1 were parallelized with OpenMP, but the NxM k-nearest search was left out. That case is now also parallelized.

• Some of the APIs from the commercial version were backported to 1.3, including the fingerprint writer API and functions for substructure fingerprint screening.

• Added and improved docstrings

This release support Python 2.7 but it no longer supports Python 2.5 or Python 2.6. The commercial version supports Python 2.7 and Python 3.5+, handles more than 4GB of fingerprint data, and has a binary fingerprint format for fast loading.

It is available from http://dalkescientific.com/releases/chemfp-1.3.tar.gz.