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A Python interface for the HOLE suite tools to analyze an ion channel pore or transporter pathway as a function of time or arbitrary order parameters.
mdahole2 is bound by a Code of Conduct.
From conda:
conda install -c conda-forge mdahole2
In case you want to use an already installed version of hole2 built from source or by installing it from conda (conda install -c conda-forge hole2), you can use a version without hole2 as dependency:
conda install -c conda-forge mdahole2-base
Or install from pip:
pip install mdahole2
Note that mdahole2 is only supported on Linux and macOS.
To build mdahole2 from source,
we highly recommend using virtual environments.
If possible, we strongly recommend that you use
Anaconda as your package manager.
Below we provide instructions both for conda and
for pip.
Ensure that you have conda installed.
Create a virtual environment and activate it:
conda create --name mdahole2
conda activate mdahole2
Install the development and documentation dependencies:
conda env update --name mdahole2 --file devtools/conda-envs/test_env.yaml --file docs/requirements.yaml
Build this package from source:
pip install -e .
If you want to update your dependencies (which can be risky!), run:
conda update --all
And when you are finished, you can exit the virtual environment with:
conda deactivate
To build the package from source, run:
pip install -e .
If you want to create a development environment, install the dependencies required for tests and docs with:
pip install -e ".[test,doc]"
The mdahole2 source code is hosted at https://github.com/MDAnalysis/mdahole2 and is available under the Lesser GNU Public Licence, v2.1 or any higher version (see the file LICENSE).
Copyright (c) 2022, The MDAnalysis Development Team and all contributors listed in the file AUTHORS
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using mdahole2 in published work.