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.

Highlights

• 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.

• Getting started: Installation | Create a fingeprint db file | Limitations

CPU searches

Learn how to run CPU based similarity searches

• CPU searches: Run Tanimoto similarity searches | Run Tversky searches with a and b parameters | Run Tversky substructure screenouts | Generate a symmetic distance matrix

GPU searches

Learn how to run GPU based similarity searches

• GPU searches: Run GPU based Tanimoto similarity searches

API documentation

• Index

• Module Index