basicrta

Name	basicrta JSON
Version	0.2.2 JSON
	download
home_page	None
Summary	A package to extract binding kinetics from molecular dynamics simulations
upload_time	2024-11-16 15:57:50
maintainer	None
docs_url	None
author	None
requires_python	>=3.10
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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)
==============================
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[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 (2024) [^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. bioRxiv. November 9, 2024. https://doi.org/10.1101/2024.11.07.622502.

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. bioRxiv. November 9, 2024. https://doi.org/10.1101/2024.11.07.622502.\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",
    "bugtrack_url": null,
    "license": "GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007  Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.  Preamble  The GNU General Public License is a free, copyleft license for software and other kinds of works.  The licenses for most software and other practical works are designed to take away your freedom to share and change the works.  By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users.  We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors.  You can apply it to your programs, too.  When we speak of free software, we are referring to freedom, not price.  Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.  To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights.  Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others.  For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received.  You must make sure that they, too, receive or can get the source code.  And you must show them these terms so they know their rights.  Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it.  For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software.  For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions.  Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so.  This is fundamentally incompatible with the aim of protecting users' freedom to change the software.  The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable.  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Definitions.  \"This License\" refers to version 3 of the GNU General Public License.  \"Copyright\" also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.  \"The Program\" refers to any copyrightable work licensed under this License.  Each licensee is addressed as \"you\".  \"Licensees\" and \"recipients\" may be individuals or organizations.  To \"modify\" a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy.  The resulting work is called a \"modified version\" of the earlier work or a work \"based on\" the earlier work.  A \"covered work\" means either the unmodified Program or a work based on the Program.  To \"propagate\" a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy.  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