mdahole2

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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.

Installation

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.

Note that mdahole2 is only supported on Linux and macOS.

With conda

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

With pip

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]"

Copyright

The mdahole2 source code is hosted at https://github.com/MDAnalysis/mdahole2 and is available under the GNU General Public License, version 3 (see the file LICENSE).

Copyright (c) 2022, The MDAnalysis Development Team and all contributors listed in the file AUTHORS

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using mdahole2 in published work.