haddock3

Official repo of the modular BioExcel version of HADDOCK

https://github.com/haddocking/haddock3

Science Score: 67.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 10 DOI reference(s) in README
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Academic publication links
Links to: biorxiv.org, nature.com, acs.org, zenodo.org
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary

Keywords

bioinformatics complexes docking integrative-modeling modelling proteins utrecht-university workflows

Last synced: 4 months ago · JSON representation ·

Repository

Official repo of the modular BioExcel version of HADDOCK

Basic Info

Host: GitHub
Owner: haddocking
License: apache-2.0
Language: Python
Default Branch: main
Homepage: https://www.bonvinlab.org/haddock3
Size: 592 MB

Statistics

Stars: 181
Watchers: 12
Forks: 50
Open Issues: 24
Releases: 11

Topics

bioinformatics complexes docking integrative-modeling modelling proteins utrecht-university workflows

Created almost 7 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

`haddock3`

PyPI - Version PyPI - Python Version

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 (assuming you have a Python version 3.9 to 3.13 installed and the rights to install the software - if not refer to the instructions in INSTALL.md for using either venv or conda) .

bash pip install haddock3

To install haddock3 with MPI support (required an OpenMPI installation - refer to the instructions in INSTALL.md use:

bash pip install 'haddock3[mpi]'

In case you rather install the latest unreleased version use instead:

bash git clone https://github.com/haddocking/haddock3.git cd haddock3 pip install .

For detailed instructions and installation of third-party software, please check INSTALL.md

You might also want to check the following utilities:

haddock-restraints: Tool to generate restraints to be used in haddock3.
haddock-runner: Tool to run large scale haddock3 simulations using multiple input molecules in different scenarios
haddock-tools: Set of useful utility scripts developed over the years by the BonvinLab group members

Usage

The most basic usage is:

bash haddock3 <configuration-file.toml>

For help on haddock3 usage:

```bash $ haddock3 -h usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe

positional arguments: recipe The input recipe file path

optional arguments: -h, --help show this help message and exit --restart RESTART Restart the run from a given step. Previous folders from the selected step onwards will be deleted. --extend-run EXTEND_RUN Start a run from a run directory previously prepared with the haddock3-copy CLI. Provide the run directory created with haddock3-copy CLI. --setup Only setup the run, do not execute --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} -v, --version show version ```

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!

Cite us

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

Research article: M. Giulini, V. Reys, J.M.C. Teixeira, B. Jiménez-García, R.V. Honorato, A. Kravchenko, X. Xu, R. Versini, A. Engel, S. Verhoeven, A.M.J.J. Bonvin, HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes Journal of Chemical Information and Modeling (2025). doi: 10.1021/acs.jcim.5c00969 [BioRxiv]
Cite this repository: M.C. Teixeira, J., Vargas Honorato, R., Giulini, M., Bonvin, A., SarahAlidoost, Reys, V., Jimenez, B., Schulte, D., van Noort, C., Verhoeven, S., Vreede, B., SSchott, & Tsai, R. (2024). haddocking/haddock3: v3.0.0-beta.5 (Version 3.0.0-beta.5) [Computer software]. https://doi.org/10.5281/zenodo.10527751

Useful resources

User manual: The online HADDOCK3 guide describing every aspects of the tool.
Best practice guide (HADDOCK2.X series)
The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes. Nature Prot. 2024

Development

Please check DEVELOPMENT for instructions on how to develop haddock3

Code Documentation

The code documentation is automatically built and hosted at bonvinlab.org/haddock3.

To build it locally it is necessary to have some extra packages installed. You can install them using the following command:

bash pip install -e '.[docs]'

Then, to build the documentation, run the following commands:

bash sphinx-apidoc -f -e -o docs/ src/haddock -d 1 sphinx-build -b html docs haddock3-docs

Warning messages are expected, but the documentation should be built successfully.

The rendered documentation will be available at haddock3-docs/index.html. This will open a local webpage with the

Contributing

Check the CONTRIBUTING file for instructions on how to contribute with the project!

Owner

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

Website: http://bonvinlab.org
Repositories: 55
Profile: https://github.com/haddocking

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: 4 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

Pull Request Labels

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

Homepage: https://github.com/haddocking/haddock3
Documentation: https://github.com/haddocking/haddock3#readme
License: Apache License 2.0
Latest release: 2025.8.0
published 5 months ago

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: 4 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

haddock3

Science Score: 67.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

haddock3

Introduction

Installation

Usage

Support

Cite us

Useful resources

Development

Code Documentation

Contributing

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: haddock3

Rankings

Maintainers (1)

Dependencies

`haddock3`