mdakithole2
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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.
mdakithole2 is bound by a Code of Conduct.
Installation
To build mdakithole2 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.
With conda
Ensure that you have conda installed.
Create a virtual environment and activate it:
conda create --name mdakithole2
conda activate mdakithole2
Install the development and documentation dependencies:
conda env update --name mdakithole2 --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 mdakithole2 source code is hosted at https://github.com/ianmkenney/hole2-mdakit and is available under the GNU General Public License, version 3 (see the file LICENSE).
Copyright (c) 2022, Ian Kenney
Acknowledgements
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using mdakithole2 in published work.