basicrta 1.2.0
A package to extract binding kinetics from molecular dynamics simulations
Requires Python: >=3.10
Keywords: molecular simulations

Bayesian Single-Cutoff Residence Time Analysis (basicrta)
==============================
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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.