Getting Started

This page details how to get started with mdahole2. Note that mdahole2 is currently only supported on Linux or macOS.

Documentation

Documentation is hosted on GitHub Pages.

Installation

mdahole2 can be installed in several ways:

From conda

The recommended way to install mdahole2 is through conda:

conda install -c conda-forge mdahole2

If you already have hole2 installed and want to use that version, you can install mdahole2 without the hole2 dependency:

conda install -c conda-forge mdahole2-base

From pip

You can also install mdahole2 using pip:

pip install mdahole2

Download and Build source code

The mdahole2 source code is hosted on GitHub and can be downloaded with

git clone [email protected]:MDAnalysis/mdahole2.git

with an SSH key, or with

git clone https://github.com/MDAnalysis/mdahole2.git

To build mdahole2 from source, we highly recommend using virtual environments, preferably with Anaconda.

With conda:

conda create --name mdahole2
conda activate mdahole2
conda env update --name mdahole2 --file devtools/conda-envs/test_env.yaml --file docs/requirements.yaml
pip install -e .

With pip:

pip install -e .

For development purposes, you can install additional test and documentation dependencies:

pip install -e ".[test,doc]"

Installing hole2

mdahole2 requires the hole2 executable to be installed.

This is most easily done using conda, mamba, or a similar package manager. For example, to install hole2 using mamba:

mamba install -c conda-forge hole2

Alternatively, hole2 can be installed from the original HOLE website.