I've written a paper describing all aspects of the chemfp project,
including the FPS and FPB file formats, methods for fast popcount
calculation and similarity search, and the experience of running
chemfp as a commercial free software project.
It's been submitted to a journal. A
is available from ChemRxiv …
Chemfp 3.3 is now available to licensed users. If you are interested
in purchasing a chemfp license, email me.
This release focused on squeezing out even more performance for
machines with the POPCNT and AVX2 instruction sets. I believe chemfp
is the fastest available single-threaded similarity search program for …
The knearest and count searches are about 10% faster. They now use a
fast integer test to reject obvious mismatches before doing the
computationally expensive divison operation. This optimization was
already available in threshold search …
I've just released
the newest version of the chemfp 1.x development track.
This version mostly contains bug fixes and internal improvements. The
biggest additions are the fpcat
command-line program, support for Dave Cosgrove's
'flush' fingerprintfile format, and support for
'fromAtoms' in some of the RDKit fingerprints …