https://github.com/mdanalysis/mdahole2
An MDAKit implementing a Python interface for the HOLE program.
https://github.com/mdanalysis/mdahole2
mdanalysis python structural-biology
Last synced: 6 months ago
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An MDAKit implementing a Python interface for the HOLE program.
- Host: GitHub
- URL: https://github.com/mdanalysis/mdahole2
- Owner: MDAnalysis
- License: lgpl-2.1
- Created: 2022-12-28T18:28:45.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-03-14T14:00:23.000Z (7 months ago)
- Last Synced: 2025-04-03T07:24:27.748Z (6 months ago)
- Topics: mdanalysis, python, structural-biology
- Language: Python
- Homepage: https://www.mdanalysis.org/mdahole2/
- Size: 15.3 MB
- Stars: 6
- Watchers: 3
- Forks: 3
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Authors: AUTHORS.md
Awesome Lists containing this project
README
mdahole2
==============================
[//]: # (Badges)
| **Latest release** | [](https://github.com/MDAnalysis/mdahole2/releases)  [](https://www.mdanalysis.org/mdahole2/)|
| :------ | :------- |
| **Status** | [](https://github.com/MDAnalysis/mdahole2/actions?query=branch%3Amain+workflow%3Agh-ci) [](https://codecov.io/gh/MDAnalysis/mdahole2/branch/main)|
| **Community** | [](https://www.mdanalysis.org) |
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](https://github.com/MDAnalysis/mdahole2/blob/main/CODE_OF_CONDUCT.md).
### Installation
From conda:
```
conda install -c conda-forge mdahole2
```
In case you want to use an already installed version of [hole2](https://www.holeprogram.org/) built from [source](https://github.com/osmart/hole2) 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.
#### From source
To build `mdahole2` from source,
we highly recommend using virtual environments.
If possible, we strongly recommend that you use
[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
Below we provide instructions both for `conda` and
for `pip`.
##### With conda
Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) 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 Lesser GNU Public Licence, v2.1 or any higher version
(see the file [LICENSE](https://github.com/MDAnalysis/mdahole2/blob/main/LICENSE)).
Copyright (c) 2022, The MDAnalysis Development Team and all contributors
listed in the file AUTHORS
#### Acknowledgements
Project based on the
[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using mdahole2 in published work.