https://github.com/chembl/FPSim2

Simple package for fast molecular similarity searches
https://github.com/chembl/FPSim2

cheminformatics chemistry gpu python similarity-search

Last synced: 2 months ago
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Simple package for fast molecular similarity searches

• Host: GitHub
• URL: https://github.com/chembl/FPSim2
• Owner: chembl
• License: mit
• Created: 2018-10-25T16:41:26.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2025-04-28T08:44:11.000Z (3 months ago)
• Last Synced: 2025-04-28T09:59:31.882Z (3 months ago)
• Topics: cheminformatics, chemistry, gpu, python, similarity-search
• Language: Python
• Homepage: https://chembl.github.io/FPSim2
• Size: 6.62 MB
• Stars: 129
• Watchers: 20
• Forks: 22
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
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[![Downloads](https://pepy.tech/badge/fpsim2)](https://pepy.tech/project/fpsim2)

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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](http://www.ebi.ac.uk/chembl/) and [SureChEMBL](https://www.surechembl.org/) interfaces.

Highlights:

- Uses CPU POPCNT instruction for fast bit counting

- Bounds for sublinear speedups from [10.1021/ci600358f](https://pubs.acs.org/doi/abs/10.1021/ci600358f)

- A compressed file format with optimised read speed based in [PyTables](https://www.pytables.org/) and [BLOSC2](http://www.blosc.org/pages/blosc-in-depth/)

- Fast multicore CPU and GPU similarity searches

- In memory and on disk search modes

- Distance matrix calculation

## Installation

With [pip](https://pypi.org/project/FPSim2/):

```bash

pip install fpsim2

```

With [conda](https://anaconda.org/conda-forge/fpsim2):

```bash

conda install conda-forge::fpsim2

```

With [SBGrid](https://sbgrid.org/software/titles/fpsim2):

```

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 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1E-Hu0YXHb4aaVQWOLzMTJFdAhh3nIbxA)