Simple package for fast molecular similarity searching

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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

pip 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 Open In Colab

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This version

0.7.3

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