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: about 1 month ago
JSON representation

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 (about 6 years ago)
• Default Branch: master
• Last Pushed: 2024-10-31T15:55:29.000Z (about 2 months ago)
• Last Synced: 2024-10-31T16:34:11.305Z (about 2 months ago)
• Topics: cheminformatics, chemistry, gpu, python, similarity-search
• Language: Python
• Homepage: https://chembl.github.io/FPSim2
• Size: 5.99 MB
• Stars: 111
• Watchers: 21
• Forks: 18
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• top-life-sciences - **chembl/FPSim2** - search`<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 104 <img src='https://github.com/HubTou/topgh/blob/main/icons/forks.png'> 17 <img src='https://github.com/HubTou/topgh/blob/main/icons/code.png'> Python <img src='https://github.com/HubTou/topgh/blob/main/icons/license.png'> MIT License <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2024-02-15 11:13:05 | (Ranked by starred repositories)

README

        
[![CI Testing](https://github.com/chembl/FPSim2/workflows/CI/badge.svg)](https://github.com/chembl/FPSim2/actions?query=workflow%3ACI+branch%3Amaster)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/fpsim2.svg)](https://anaconda.org/conda-forge/fpsim2)

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

[![DOI](https://zenodo.org/badge/154705090.svg)](https://zenodo.org/badge/latestdoi/154705090)

# 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/) interface.

Highlights:

- Using CPU POPCNT instruction

- 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 [BLOSC](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

```bash

pip install fpsim2

```

or

```bash

conda install -c conda-forge fpsim2

```

## Documentation

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

## Trying it online

To try out FPSim2 interactively in your web browser, just click on the binder icon [![Binder](http://mybinder.org/badge.svg)](http://beta.mybinder.org/v2/gh/eloyfelix/fpsim2_binder/master?filepath=demo.ipynb)