FPSim2: Simple package for fast molecular similarity searches

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

Highlights:

• Uses CPU POPCNT instruction for fast bit counting
• Bounds for sublinear speedups from 10.1021/ci600358f
• A compressed file format with optimised read speed based in PyTables and BLOSC2
• Fast multicore CPU and GPU similarity searches
• In memory and on disk search modes
• Distance matrix calculation

Installation

With pip:

pip install fpsim2

With conda:

conda install conda-forge::fpsim2

With SBGrid:

sbgrid-cli install fpsim2

Documentation

Documentation is available at https://chembl.github.io/FPSim2/

Trying it online

To try out FPSim2 interactively in your web browser, check out this Google Colab notebook