chemfp 1.3 is available

This release has been updated to handle the most recent versions of RDKit, Open Babel, and OEChem/OEGraphSim. This includes detection of the new MACCS versions they all implement (key 44 was missing), and support for RDKit’s Avalon and pattern fingerprints.

There is some general performance tuning. The FPS parser is about 40% faster and the MACCS search is about 30% faster. In addition, the NxM k-nearest search is now parallelized. Somehow I left it out when I added OpenMP support in ...

Continue Reading →

chemfp-1.1 is available

If you’ve still using chemfp-1.0 then have I got a treat for you! The new release includes many performance optimizations. When chemfp starts, it looks at your CPU to figure out the fastest popcount method. The built-in POPCNT instruction is about 4x faster than the byte table lookup. It can use OpenMP to take advantage of multiple cores. There’s even special functions for symmetric searches. On some benchmarks, the new code is 30x faster than the old one.

There are other ...

Continue Reading →