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haddock3

Official repo of the modular BioExcel version of HADDOCK

https://github.com/haddocking/haddock3

Science Score: 41.0%

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org, nature.com, acs.org, zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.9%) to scientific vocabulary

Keywords

bioinformatics complexes docking integrative-modeling modelling proteins utrecht-university workflows
Last synced: about 1 month ago · JSON representation ·

Repository

Official repo of the modular BioExcel version of HADDOCK

Basic Info
Statistics
  • Stars: 181
  • Watchers: 12
  • Forks: 50
  • Open Issues: 24
  • Releases: 11
Topics
bioinformatics complexes docking integrative-modeling modelling proteins utrecht-university workflows
Created over 7 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

haddock3-logo

DOI Research Software Directory fair-software.eu OpenSSF Best Practices

Downloads PyPI - Version PyPI - Python Version SBGrid Badge

ci pages CodeQL Codacy Badge Codacy Badge

Introduction

HADDOCK, standing for High Ambiguity Driven protein-protein DOCKing, is a widely used computational tool for the integrative modeling of biomolecular interactions. Developed by researchers at Utrecht University in the BonvinLab for more than 20 years, it integrates various types of experimental data, biochemical, biophysical, bioinformatic prediction and knowledge to guide the docking process.

Installation

Simple installation of the latest release of HADDOCK3 (requires Python 3.10+):

bash pip install haddock3

For Python environment setup and installation instructions, see docs/PYTHON.md.

For development installation or to install the latest unreleased version please refer to docs/DEVELOPMENT.md

Usage

The most basic usage is:

bash haddock3 <configuration-file.toml>

Check the EXAMPLES page for more some usage examples and the User manual for a more detailed explanation of the configuration file.

Support

If you encounter any code-related issues, please open an issue.

If you have any other questions or need help, please contact us at ask.bioexcel.eu.

If you clone this repository and use haddock3 for your research, please support us by signing up in this form. This will allow us contact you when needed for haddock3-related issues, and also provide us a mean to demonstrate impact when reporting for grants - which grealty helps us to keep the project alive!

Useful resources

Development

For development setup and guidelines, see docs/DEVELOPMENT.md.

Contributing

See CONTRIBUTING.md

Cite us

If you used haddock3 for your research, please cite us:

Owner

  • Name: HADDOCK
  • Login: haddocking
  • Kind: organization
  • Location: Utrecht, The Netherlands

Computational Structural Biology Group @ Utrecht University

Citation (CITATION.cff) 

# YAML 1.2
# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
cff-version: 1.2.0
message: "If you use this software, please cite it using these metadata."
# FIXME title as repository name might not be the best name, please make human readable
title: 'HADDOCK3 - modular integrative modelling software'
doi: 10.5281/zenodo.10527751
# FIXME splitting of full names is error prone, please check if given/family name are correct
authors:
- given-names: Joao
  family-names: Teixeira
  name-particle: M.C.
  affiliation: Zymvol
- given-names: Rodrigo
  family-names: Honorato
  name-particle: Vargas
  affiliation: '@UtrechtUniversity'
- given-names: Marco
  family-names: Giulini
  affiliation: Utrecht University
- given-names: Alexandre
  family-names: Bonvin
  affiliation: '@UtrechtUniversity'
- given-names: Sarah
  family-names: Alidoost
  affiliation: Netherlands eScience center
- given-names: Victor
  family-names: Reys
  affiliation: '@haddocking'
- given-names: Brian
  family-names: Jimenez
  affiliation: '@zymvol'
- given-names: Douwe
  family-names: Schulte
  affiliation: '@UtrechtUniversity'
- given-names: Charlotte
  family-names: van Noort
  affiliation: Utrecht University
- given-names: Stefan
  family-names: Verhoeven
  affiliation: Netherlands eScience Center
- given-names: Barbara
  family-names: Vreede
- given-names: SSchott
- given-names: Regen
  family-names: Tsai
version: "2024.10.0b6"
date-released: 2024-01-18
repository-code: https://github.com/haddocking/haddock3
license: CC-BY-4.0

GitHub Events

Total
  • Create event: 126
  • Release event: 3
  • Issues event: 177
  • Watch event: 61
  • Delete event: 118
  • Issue comment event: 335
  • Push event: 688
  • Pull request review comment event: 209
  • Pull request event: 241
  • Pull request review event: 359
  • Fork event: 14
Last Year
  • Create event: 126
  • Release event: 3
  • Issues event: 177
  • Watch event: 61
  • Delete event: 118
  • Issue comment event: 335
  • Push event: 688
  • Pull request review comment event: 209
  • Pull request event: 241
  • Pull request review event: 359
  • Fork event: 14

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 240
  • Total pull requests: 321
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 18 days
  • Total issue authors: 40
  • Total pull request authors: 11
  • Average comments per issue: 1.48
  • Average comments per pull request: 0.86
  • Merged pull requests: 221
  • Bot issues: 0
  • Bot pull requests: 62
Past Year
  • Issues: 125
  • Pull requests: 202
  • Average time to close issues: 8 days
  • Average time to close pull requests: 5 days
  • Issue authors: 27
  • Pull request authors: 8
  • Average comments per issue: 1.67
  • Average comments per pull request: 0.56
  • Merged pull requests: 135
  • Bot issues: 0
  • Bot pull requests: 62
View more stats
Top Authors
Issue Authors
  • VGPReys (54)
  • mgiulini (53)
  • amjjbonvin (38)
  • rvhonorato (29)
  • sverhoeven (9)
  • 187357181 (8)
  • AnnaKravchenko (5)
  • alchemistcai (4)
  • LiviaPham (4)
  • bestz123 (3)
  • EricDeveaud (2)
  • pallavi-compchem (2)
  • jh2ee (2)
  • wifeofbrutus (1)
  • ahmedselim2017 (1)
Pull Request Authors
  • VGPReys (76)
  • dependabot[bot] (62)
  • mgiulini (62)
  • rvhonorato (52)
  • amjjbonvin (50)
  • sverhoeven (6)
  • AnnaKravchenko (5)
  • rversin (5)
  • SarahAlidoost (1)
  • alchemistcai (1)
  • joaomcteixeira (1)
Top Labels
Issue Labels
enhancement (116) bug (58) community (32) execution (19) question (18) m|caprieval (12) feature (11) CNS (11) documentation (10) analysis/postprocessing (10) CI / repository (10) discussions (7) m|rigidbody (7) workflow (7) m|mdref (6) m|flexref (6) m|mdscoring (6) m|alascan (6) yaml default parameters (6) parameters-topologies (5) m|emref (5) m|emscoring (5) examples (5) m|topoaa (4) m|seletopclusts (3) m|clustfcc (3) m|clustrmsd (3) m|contactmap (3) m|ilrmsdmatrix (3) m|openmm (2)
Pull Request Labels
dependencies (63) enhancement (61) bug (41) CNS (22) python (20) m|rigidbody (16) CI / repository (14) feature (14) m|caprieval (14) parameters-topologies (13) m|topoaa (12) community (12) documentation (12) execution (11) analysis/postprocessing (11) m|flexref (10) m|emscoring (9) m|mdscoring (9) m|topocg (9) workflow (8) m|emref (7) m|mdref (7) m|clustfcc (5) m|clustrmsd (5) m|ilrmsdmatrix (5) examples (4) yaml default parameters (4) m|seletopclusts (4) m|alascan (4) m|openmm (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 403 last-month
  • Total docker downloads: 9
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
pypi.org: haddock3

HADDOCK3

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 403 Last month
  • Docker Downloads: 9
Rankings
Dependent packages count: 10.2%
Average: 33.9%
Dependent repos count: 57.5%
Maintainers (1)
bonvinlab
Last synced: 11 months ago

Dependencies

devtools/docs-requirements.txt pypi
  • CommonMark *
  • jsonpickle *
  • mock *
  • myst-parser *
  • sphinx >=2
  • sphinx-argparse *
  • sphinx-rtd-theme *
requirements.txt pypi
  • biopython ==1.79
  • jsonpickle ==2.1.0
  • numpy ==1.22.2
  • pdb-tools ==2.4.5
  • pyyaml ==6.0
  • scipy ==1.8.0
  • tox ==3.24.5
setup.py pypi
  • not *
.github/workflows/docs.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/pages.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v4 composite
  • s0/git-publish-subdir-action develop composite
.github/workflows/tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v2 composite
.github/workflows/github-to-gitlab-push-sync.yml actions
  • actions/checkout v4 composite
  • haddocking/haddock3 main composite
action.yml actions