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https://github.com/becksteinlab/basicrta
https://github.com/becksteinlab/basicrta
Last synced: 10 days ago
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- Host: GitHub
- URL: https://github.com/becksteinlab/basicrta
- Owner: Becksteinlab
- License: gpl-3.0
- Created: 2023-12-20T23:01:46.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2024-10-24T20:41:07.000Z (27 days ago)
- Last Synced: 2024-10-26T07:49:25.194Z (25 days ago)
- Language: Python
- Size: 6.9 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 2
-
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
Bayesian Single-Cutoff Residence Time Analysis (basicrta)
==============================
[//]: # (Badges)
| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since] [![Documentation Status][badge_docs]][url_docs]|
| :----------------- | :------- |
| **Archives** | [![DOI][badge_zenodo]][url_zenodo] |
| **Status** | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
| **Community** | [![License: GPL v3][badge_license]][url_license] [![Powered by MDAnalysis][badge_mda]][url_mda]|
[badge_actions]: https://github.com/becksteinlab/basicrta/actions/workflows/gh-ci.yaml/badge.svg
[badge_codecov]: https://codecov.io/gh/becksteinlab/basicrta/branch/main/graph/badge.svg
[badge_commits_since]: https://img.shields.io/github/commits-since/becksteinlab/basicrta/latest
[badge_docs]: https://readthedocs.org/projects/basicrta/badge/?version=latest
[badge_license]: https://img.shields.io/badge/License-GPLv3-blue.svg
[badge_zenodo]: https://zenodo.org/badge/DOI/10.5281/zenodo.13877225.svg
[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,AAABAAEAEBAAAAEAIAAoBAAAFgAAACgAAAAQAAAAIAAAAAEAIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJD+XwCY/fEAkf3uAJf97wGT/a+HfHaoiIWE7n9/f+6Hh4fvgICAjwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACT/yYAlP//AJ///wCg//8JjvOchXly1oaGhv+Ghob/j4+P/39/f3IAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJH8aQCY/8wAkv2kfY+elJ6al/yVlZX7iIiI8H9/f7h/f38UAAAAAAAAAAAAAAAAAAAAAAAAAAB/f38egYF/noqAebF8gYaagnx3oFpUUtZpaWr/WFhY8zo6OmT///8BAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAgICAn46Ojv+Hh4b/jouJ/4iGhfcAAADnAAAA/wAAAP8AAADIAAAAAwCj/zIAnf2VAJD/PAAAAAAAAAAAAAAAAICAgNGHh4f/gICA/4SEhP+Xl5f/AwMD/wAAAP8AAAD/AAAA/wAAAB8Aov9/ALr//wCS/Z0AAAAAAAAAAAAAAACBgYGOjo6O/4mJif+Pj4//iYmJ/wAAAOAAAAD+AAAA/wAAAP8AAABhAP7+FgCi/38Axf4fAAAAAAAAAAAAAAAAiIiID4GBgYKCgoKogoB+fYSEgZhgYGDZXl5e/m9vb/9ISEjpEBAQxw8AAFQAAAAAAAAANQAAADcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAjo6Mb5iYmP+cnJz/jY2N95CQkO4pKSn/AAAA7gAAAP0AAAD7AAAAhgAAAAEAAAAAAAAAAACL/gsAkv2uAJX/QQAAAAB9fX3egoKC/4CAgP+NjY3/c3Nz+wAAAP8AAAD/AAAA/wAAAPUAAAAcAAAAAAAAAAAAnP4NAJL9rgCR/0YAAAAAfX19w4ODg/98fHz/i4uL/4qKivwAAAD/AAAA/wAAAP8AAAD1AAAAGwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALGxsVyqqqr/mpqa/6mpqf9KSUn/AAAA5QAAAPkAAAD5AAAAhQAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADkUFBSuZ2dn/3V1df8uLi7bAAAATgBGfyQAAAA2AAAAMwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAB0AAADoAAAA/wAAAP8AAAD/AAAAWgC3/2AAnv3eAJ/+dgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA9AAAA/wAAAP8AAAD/AAAA/wAKDzEAnP3WAKn//wCS/OgAf/8MAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIQAAANwAAADtAAAA7QAAAMAAABUMAJn9gwCe/e0Aj/2LAP//AQAAAAAAAAAA
[badge_release]: https://img.shields.io/github/release-pre/becksteinlab/basicrta.svg
[url_actions]: https://github.com/becksteinlab/basicrta/actions?query=branch%3Amain+workflow%3Agh-ci
[url_codecov]: https://codecov.io/gh/becksteinlab/basicrta/branch/main
[url_docs]: https://basicrta.readthedocs.io/en/latest/?badge=latest
[url_latest_release]: https://github.com/becksteinlab/basicrta/releases
[url_license]: https://www.gnu.org/licenses/gpl-2.0
[url_mda]: https://www.mdanalysis.org
[url_zenodo]: https://doi.org/10.5281/zenodo.13877225
A package to extract binding kinetics from molecular dynamics simulations
basicrta is bound by a [Code of Conduct](https://github.com/becksteinlab/basicrta/blob/main/CODE_OF_CONDUCT.md).
### Installation
To build basicrta 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 basicrta
conda activate basicrta
```
Install the development and documentation dependencies:
```
conda env update --name basicrta --file devtools/conda-envs/test_env.yaml
conda env update --name basicrta --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 .
```
If you want to create a development environment, install
the dependencies required for tests and docs with:
```
pip install ".[test,doc]"
```
### Copyright
The basicrta source code is hosted at https://github.com/becksteinlab/basicrta
and is available under the GNU General Public License, version 3 (see the file [LICENSE](https://github.com/becksteinlab/basicrta/blob/main/LICENSE)).
Copyright (c) 2024, Ricky Sexton
#### 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 basicrta in published work.