Welcome to FPSim2’s documentation!

FPSim2 is a small NumPy centric Python/C++ package to run fast compound similarity searches. FPSim2 performs better with high search thresholds (>=0.7). Currently used in the ChEMBL interface.


  • Using CPU POPCNT instruction

  • Bounds for sublinear speedups from 10.1021/ci600358f

  • A compressed file format with optimised read speed based in PyTables and BLOSC

  • Fast multicore CPU and GPU similarity searches

  • In memory and on disk search modes

  • Distance matrix calculation

Getting started

Install and generate a FPSim2 fingerprint db file.

GPU searches

Learn how to run GPU based similarity searches

API documentation