| Name | basicrta JSON |
| Version |
1.1.1
JSON |
| download |
| home_page | None |
| Summary | A package to extract binding kinetics from molecular dynamics simulations |
| upload_time | 2025-07-19 00:09:49 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | None |
| keywords |
molecular
simulations
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
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
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[badge_release]: https://img.shields.io/github/release-pre/becksteinlab/basicrta.svg
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[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 based
on Sexton (2025) [^1].
[^1]: Sexton, R.; Fazel, M.; Schweiger, M.; Pressé, S.; Beckstein, O. Bayesian Nonparametric Analysis of Residence Times for
Protein-Lipid Interactions in Molecular Dynamics Simulations. *Journal of Chemical Theory and Computation*
**2025** *21* (8), 4203-4220
DOI: `10.1021/acs.jctc.4c01522 <http://doi.org/10.1021/acs.jctc.4c01522>`_
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.
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Bayesian Nonparametric Analysis of Residence Times for \n Protein-Lipid Interactions in Molecular Dynamics Simulations. *Journal of Chemical Theory and Computation* \n **2025** *21* (8), 4203-4220\n DOI: `10.1021/acs.jctc.4c01522 <http://doi.org/10.1021/acs.jctc.4c01522>`_ \n\nbasicrta is bound by a [Code of Conduct](https://github.com/becksteinlab/basicrta/blob/main/CODE_OF_CONDUCT.md).\n\n### Installation\n\nTo build basicrta from source,\nwe highly recommend using virtual environments.\nIf possible, we strongly recommend that you use\n[Anaconda](https://docs.conda.io/en/latest/) as your package manager.\nBelow we provide instructions both for `conda` and\nfor `pip`.\n\n#### With conda\n\nEnsure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.\n\nCreate a virtual environment and activate it:\n\n```\nconda create --name basicrta\nconda activate basicrta\n```\n\nInstall the development and documentation dependencies:\n\n```\nconda env update --name basicrta --file devtools/conda-envs/test_env.yaml\nconda env update --name basicrta --file docs/requirements.yaml\n```\n\nBuild this package from source:\n\n```\npip install -e .\n```\n\nIf you want to update your dependencies (which can be risky!), run:\n\n```\nconda update --all\n```\n\nAnd when you are finished, you can exit the virtual environment with:\n\n```\nconda deactivate\n```\n\n#### With pip\n\nTo build the package from source, run:\n\n```\npip install .\n```\n\nIf you want to create a development environment, install\nthe dependencies required for tests and docs with:\n\n```\npip install \".[test,doc]\"\n```\n\n### Copyright\n\nThe basicrta source code is hosted at https://github.com/becksteinlab/basicrta\nand is available under the GNU General Public License, version 3 (see the file [LICENSE](https://github.com/becksteinlab/basicrta/blob/main/LICENSE)).\n\nCopyright (c) 2024, Ricky Sexton\n\n\n#### Acknowledgements\n \nProject based on the \n[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.\nPlease cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using basicrta in published work.\n",
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