Bayesian Single-Cutoff Residence Time Analysis (basicrta)

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A package to extract binding kinetics from molecular dynamics simulations based on Sexton (2024) ¹.

basicrta is bound by a Code of Conduct.

Installation

To build basicrta 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 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).

Copyright (c) 2024, Ricky Sexton

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using basicrta in published work.

Footnotes

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. bioRxiv. November 9, 2024. https://doi.org/10.1101/2024.11.07.622502. ↩