chemfp 1.3 released
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.