FPSim2's documentation
FPSim2 is a NumPy-centric Python/C++ package for running fast compound similarity searches. FPSim2 performs optimally with high search thresholds (>=0.7). It is currently used in the ChEMBL and SureChEMBL interfaces.
Highlights
- Uses SIMD instructions
- Implements bounds for sublinear speedups from 10.1021/ci600358f
- Features a compressed file format with optimized read speed based on PyTables and BLOSC
- Provides fast multicore CPU and GPU similarity searches
- Supports in-memory and on-disk search modes
- Enables distance matrix calculation
Getting started
Install and generate a FPSim2 fingerprint db file.
CPU searches
Learn how to run CPU based similarity searches:
- Run symmetric similarity searches
- Run Tversky asymmetric searches
- Run substructure screenouts
- Generate a symmetric distance matrix
GPU searches
Learn how to run GPU based similarity searches: