Simple package for fast molecular similarity searching

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  • License: MIT License (MIT)
  • Author: Eloy Felix
  • Requires: Python >=3.8
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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 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

Installation

pip install fpsim2

or

conda install -c conda-forge fpsim2

Documentation

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

Trying it online

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  • License: MIT License (MIT)
  • Author: Eloy Felix
  • Requires: Python >=3.8
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Release history Release notifications | RSS feed

0.7.3

0.7.2

0.7.1

0.7.0

0.6.2

0.6.1

0.6.0

0.5.2

0.5.1

0.5.0

0.4.5

0.4.4

This version

0.4.3

0.4.2

0.4.1

0.4.0

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