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A package to extract binding kinetics from molecular dynamics simulations based on [Sexton_2024].
.. [Sexton_2024] Sexton, R.; Fazel, M.; Schweiger, M.; Pressé, S.; Beckstein, O. Bayesian Nonparametric Analysis of Residence Times for Protein-Lipid Interactions in Molecular Dynamics Simulations. November 9, 2024. https://doi.org/10.1101/2024.11.07.622502.
basicrta is bound by a Code of Conduct.
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.
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
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]"
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
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using basicrta in published work.