Installation

Create a virtual environment with Python 3.9:

You can use Python’s venv or conda depending on your choice. Commands are provided below:

with venv

python -m venv .venv
source .venv/bin/activate

with conda

conda create -n haddock3 python=3.9
conda activate haddock3

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

(Optional) Install MPI libraries if you intend to run HADDOCK3 with MPI

To use the mpi implementation of haddock3 you must have mpi4py installed in the (haddock3) python environment, and OpenMPI in the host system.

$ pip install mpi4py
# or
$ conda install -c conda-forge mpi4py

Later, you can find here instructions on how to run HADDOCK3 with MPI.

Troubleshooting the CNS executable

Depending on your architecture, the CNS executable coming with the pip install command (see above), might give errors because of some missing libraries. In such a case you should recompile CNS (see the CNS.md file in the docs directory). Once you have tested your newly compiled executable you can place it in the install haddock3 version. For this do the following:

  1. First get the location where haddock3 has been installed, e.g.:

> pip show haddock3
Name: haddock3
Version: 2024.10.0b7
Summary: HADDOCK3
Home-page:
Author:
Author-email: BonvinLab <bonvinlab.support@uu.nl>
License: Apache License 2.0
Location: /home/testuser/.venv/lib/python3.9/site-packages
...

  1. Copy your CNS executable to the haddock3 installation:

> cp <my-cns-binary> /home/testuser/.venv/lib/python3.9/site-packages/haddock/bin/cns

(Optional) Install web service dependencies if you intend to run HADDOCK3 restraints web service

To run the restraints web service you must have the following dependencies installed in the (haddock3) python environment:

pip install uvicorn fastapi

Information on the restraints web service can be found here.

Installing third-party packages

HADDOCK3 can integrate third-party software in its workflows. We are not responsible for the proper installation of such packages, but we help you install them. Below, you will find a list of all third-party packages HADDOCK3 can use and guidelines for their proper installation.

lightdock (outdated)

To install lightdock follow the instructions on the project’s website. Remember to install it under the same Python environment you created for HADDOCK3. If you have any doubts, please let us know.

gdock (outdated)

  1. Clone the latest version:

cd some-folder
git clone https://github.com/rvhonorato/gdock.git

  1. Install Python3+ dependencies

pip install deap scipy mgzip biopython

  1. Set GDOCK_PATH

export GDOCK_PATH=some-folder

Important: These are not the full gdock installation instructions as only the model generation is used here. Please check the repository page for more information.

openmm

The use of the openmm module requires the installation of both OpenMM and pdbfixer.

In venv

The venv installation instruction uses pip and requires a python version >=3.10 (not functional with python3.9).

# Create a new virtual env
python3.12 -m venv hd3-openmm
source hd3-openmm/bin/activate
# Install haddock3
pip install .
# Install OpenMM
pip install openmm==8.2.0
# Install openmm - pdbfixer
pip install https://github.com/openmm/pdbfixer/archive/refs/tags/v1.10.tar.gz

In conda

The Conda installation instructions are using conda-forge to retrieve packages and requires a python3 version between 3.9 and 3.13.

conda create -n hd3-p39-openmm python=3.9
# Activate the haddock3 env
conda activate hd3-p39-openmm
# Install haddock3
pip install haddock3
# libstdxx must be installed, maybe already present in your system
conda install -c conda-forge libstdcxx-ng
# Install OpenMM and related tools/binaries
conda install -c conda-forge openmm==8.2.0 pdbfixer==1.10

OpenMM should automatically detect the fastest platform among those available on your machine.

Please refer to the official page of the project for a full description of the installation procedure.