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prolif

Interaction Fingerprints for protein-ligand complexes and more

https://github.com/chemosim-lab/prolif

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary

Keywords

cheminformatics docking drug-design drug-discovery mdanalysis molecular-dynamics rdkit

Keywords from Contributors

computational-chemistry molecular-dynamics-simulation molecular-simulation trajectory-analysis
Last synced: 6 months ago · JSON representation ·

Repository

Interaction Fingerprints for protein-ligand complexes and more

Basic Info
  • Host: GitHub
  • Owner: chemosim-lab
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Homepage: https://prolif.readthedocs.io
  • Size: 11.5 MB
Statistics
  • Stars: 437
  • Watchers: 14
  • Forks: 84
  • Open Issues: 24
  • Releases: 13
Topics
cheminformatics docking drug-design drug-discovery mdanalysis molecular-dynamics rdkit
Created about 6 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.rst 

ProLIF
======

.. list-table::
    :widths: 12 35

    * - **Documentation**
      - |docs|
    * - **CI**
      - |tests| |codecov| |codeql|
    * - **Builds**
      - |conda-version| |pypi-version| |build|
    * - **Dependencies**
      - |mdanalysis| |rdkit|
    * - **License**
      - |license|

Description
-----------

ProLIF (*Protein-Ligand Interaction Fingerprints*) is a tool designed to generate
interaction fingerprints for complexes made of ligands, protein, DNA or RNA molecules
extracted from molecular dynamics trajectories, docking simulations and experimental
structures.

Documentation
-------------

The installation instructions, documentation and tutorials can be found online on
`ReadTheDocs `_.

Issues
------

If you have found a bug, please open an issue on the
`GitHub Issues `_ page.

Discussion
----------

If you have questions on how to use ProLIF, or if you want to give feedback or share
ideas and new features, please head to the
`GitHub Discussions `_ page.

Contributing
------------

If you are interested in contributing to the project, please read the
`Contribution Guidelines `_.

Citing ProLIF
-------------

Please refer to the `citation page `_
on the documentation.

License
-------

Unless otherwise noted, all files in this directory and all subdirectories are
distributed under the Apache License, Version 2.0 ::

    Copyright 2017-2025 Cédric BOUYSSET

    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
    You may obtain a copy of the License at

        http://www.apache.org/licenses/LICENSE-2.0

    Unless required by applicable law or agreed to in writing, software
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
    limitations under the License.


.. |pypi-version| image:: https://img.shields.io/pypi/v/prolif.svg
   :target: https://pypi.python.org/pypi/prolif
   :alt: Pypi Version

.. |conda-version| image:: https://img.shields.io/conda/vn/conda-forge/prolif.svg
    :target: https://anaconda.org/conda-forge/prolif
    :alt: Conda-forge version

.. |build| image:: https://github.com/chemosim-lab/ProLIF/workflows/build/badge.svg
    :target: https://github.com/chemosim-lab/ProLIF/actions/workflows/build.yml
    :alt: Build status

.. |tests| image:: https://github.com/chemosim-lab/ProLIF/workflows/tests/badge.svg?branch=master
    :target: https://github.com/chemosim-lab/ProLIF/actions/workflows/ci.yml
    :alt: Tests status

.. |codecov| image:: https://codecov.io/gh/chemosim-lab/ProLIF/branch/master/graph/badge.svg?token=2FCHV08G8A
    :target: https://codecov.io/gh/chemosim-lab/ProLIF

.. |docs| image:: https://readthedocs.org/projects/prolif/badge/?version=latest
    :target: https://prolif.readthedocs.io/
    :alt: Documentation Status

.. |codeql| image:: https://github.com/chemosim-lab/ProLIF/workflows/CodeQL/badge.svg?branch=master
    :target: https://github.com/chemosim-lab/ProLIF/actions/workflows/codeql.yml
    :alt: Code quality

.. |license| image:: https://img.shields.io/pypi/l/prolif
    :target: http://www.apache.org/licenses/LICENSE-2.0
    :alt: License

.. |mdanalysis| image:: https://img.shields.io/badge/Powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
    :alt: Powered by MDAnalysis
    :target: https://www.mdanalysis.org

.. |rdkit| image:: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC
      :alt: Powered by RDKit
      :target: https://www.rdkit.org/

Owner

  • Name: ChemSenSim Lab
  • Login: chemosim-lab
  • Kind: organization
  • Location: Nice, France

Chemical Senses & Simulations

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite the corresponding article (see preferred-citation)."
authors: 
  -
    family-names: Bouysset
    given-names: "Cédric"
    orcid: "https://orcid.org/0000-0002-7814-8158"
repository-code: "https://github.com/chemosim-lab/ProLIF"
title: "ProLIF"
license: Apache-2.0
preferred-citation:
  authors:
    -
      family-names: Bouysset
      given-names: "Cédric"
      orcid: "https://orcid.org/0000-0002-7814-8158"
    -
      family-names: Fiorucci
      given-names: "Sébastien"
      orcid: "https://orcid.org/0000-0003-2245-0478"
  title: "ProLIF: a library to encode molecular interactions as fingerprints"
  type: article
  doi: "10.1186/s13321-021-00548-6"
  issn: "1758-2946"
  year: 2021
  date-published: "2021-09-25"
  volume: 13
  issue: 1
  start: 72
  journal: "Journal of Cheminformatics"

GitHub Events

Total
  • Create event: 14
  • Commit comment event: 1
  • Issues event: 61
  • Watch event: 62
  • Delete event: 11
  • Member event: 2
  • Issue comment event: 222
  • Push event: 106
  • Pull request review comment event: 130
  • Pull request review event: 71
  • Pull request event: 52
  • Fork event: 17
Last Year
  • Create event: 14
  • Commit comment event: 1
  • Issues event: 61
  • Watch event: 62
  • Delete event: 11
  • Member event: 2
  • Issue comment event: 222
  • Push event: 106
  • Pull request review comment event: 130
  • Pull request review event: 71
  • Pull request event: 52
  • Fork event: 17

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 149
  • Total Committers: 8
  • Avg Commits per committer: 18.625
  • Development Distribution Score (DDS): 0.242
Past Year
  • Commits: 59
  • Committers: 4
  • Avg Commits per committer: 14.75
  • Development Distribution Score (DDS): 0.068
Top Committers
Name Email Commits
Cédric Bouysset b****c@g****m 113
Cédric Bouysset c****t@u****r 29
Irfan Alibay I****y 2
Muhammad Radifar m****5@g****m 1
readthedocs-assistant 9****t 1
Pavel p****k@u****t 1
lgtm-com[bot] 4****] 1
ReneH 4****3 1
Committer Domains (Top 20 + Academic)
ukr.net: 1 unice.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 173
  • Total pull requests: 86
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 16 days
  • Total issue authors: 98
  • Total pull request authors: 18
  • Average comments per issue: 2.42
  • Average comments per pull request: 2.74
  • Merged pull requests: 67
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 38
  • Pull requests: 55
  • Average time to close issues: 6 days
  • Average time to close pull requests: 22 days
  • Issue authors: 26
  • Pull request authors: 9
  • Average comments per issue: 1.47
  • Average comments per pull request: 3.09
  • Merged pull requests: 38
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cbouy (16)
  • xavgit (7)
  • ale94mleon (5)
  • ONISniperOne (5)
  • Le-Phung-Hien (5)
  • cbouysset (4)
  • noahharrison64 (4)
  • askusay (3)
  • forcefield (3)
  • andresilvapimentel (3)
  • DrrDom (3)
  • mljchen102 (3)
  • Anujkumarp (3)
  • rwxayheee (3)
  • Lili-Cao (3)
Pull Request Authors
  • cbouy (47)
  • nilay-v3rma (10)
  • talagayev (8)
  • yuyuan871111 (5)
  • H-EKE (4)
  • amorehead (4)
  • cbouysset (3)
  • exs-cbouy (2)
  • VAKozyrev (2)
  • wehs7661 (2)
  • asiomchen (2)
  • readthedocs-assistant (1)
  • ReneHamburger1993 (1)
  • jtwang1027 (1)
  • IAlibay (1)
Top Labels
Issue Labels
enhancement (12) bug (8) visualization (8) documentation (7) question (2) good first issue (2) multiprocessing (1) how-to-use (1) invalid (1) duplicate (1) wontfix (1) awaiting-feedback (1) low-priority (1)
Pull Request Labels
bug (1)

Packages

  • Total packages: 4
  • Total downloads:
    • pypi 6,865 last-month
  • Total docker downloads: 10
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 5
    (may contain duplicates)
  • Total versions: 49
  • Total maintainers: 1
pypi.org: prolif

Interaction Fingerprints for protein-ligand complexes and more

  • Homepage: https://github.com/chemosim-lab/ProLIF
  • Documentation: https://prolif.readthedocs.io/en/stable/
  • License: Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. 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  • Latest release: 2.0.3
    published almost 2 years ago
  • Versions: 25
  • Dependent Packages: 2
  • Dependent Repositories: 4
  • Downloads: 6,865 Last month
  • Docker Downloads: 10
Rankings
Dependent packages count: 3.2%
Stargazers count: 3.7%
Docker downloads count: 4.1%
Average: 4.9%
Downloads: 5.3%
Forks count: 5.4%
Dependent repos count: 7.5%
Maintainers (1)
cbouy
Last synced: 6 months ago
proxy.golang.org: github.com/chemosim-lab/ProLIF
  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/chemosim-lab/prolif
  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
conda-forge.org: prolif
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 24.4%
Stargazers count: 25.4%
Forks count: 25.9%
Average: 31.8%
Dependent packages count: 51.6%
Last synced: 6 months ago

Dependencies

.github/workflows/build.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite
.binder/environment.yml pypi
  • py3Dmol *
  • pyvis *