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https://github.com/becksteinlab/rmsfkit

Last synced: 10 days ago
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Host: GitHub
URL: https://github.com/becksteinlab/rmsfkit
Owner: Becksteinlab
License: gpl-2.0
Created: 2023-03-20T02:49:01.000Z (over 1 year ago)
Default Branch: main
Last Pushed: 2023-04-13T21:13:48.000Z (over 1 year ago)
Last Synced: 2024-03-25T23:15:55.019Z (8 months ago)
Language: Python
Size: 55.7 KB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Authors: AUTHORS.md

Awesome Lists containing this project

README

        rmsfkit

==============================

[//]: # (Badges)

| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/ianmkenney/rmsfkit.svg)](https://github.com/ianmkenney/rmsfkit/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/ianmkenney/rmsfkit/latest)  [![Documentation Status](https://readthedocs.org/projects/rmsfkit/badge/?version=latest)](https://rmsfkit.readthedocs.io/en/latest/?badge=latest)|

| :------ | :------- |

| **Status** | [![GH Actions Status](https://github.com/ianmkenney/rmsfkit/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/ianmkenney/rmsfkit/actions?query=branch%3Amain+workflow%3Agh-ci) [![codecov](https://codecov.io/gh/ianmkenney/rmsfkit/branch/main/graph/badge.svg)](https://codecov.io/gh/ianmkenney/rmsfkit/branch/main) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/ianmkenney/rmsfkit.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/ianmkenney/rmsfkit/context:python) |

| **Community** | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)  [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)|

A package to perform RMSF analysis on molecular dynamics data.

rmsfkit is bound by a [Code of Conduct](https://github.com/ianmkenney/rmsfkit/blob/main/CODE_OF_CONDUCT.md).

### Installation

To build rmsfkit 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 rmsfkit

conda activate rmsfkit

```

Install the development and documentation dependencies:

```

conda env update --name rmsfkit --file devtools/conda-envs/test_env.yaml

conda env update --name rmsfkit --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 -e .

```

If you want to create a development environment, install

the dependencies required for tests and docs with:

```

pip install -e ".[test,doc]"

```

### Copyright

The rmsfkit source code is hosted at https://github.com/ianmkenney/rmsfkit

and is available under the GNU General Public License, version 3 (see the file [LICENSE](https://github.com/ianmkenney/rmsfkit/blob/main/LICENSE)).

Copyright (c) 2023, Ian Kenney

#### 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 rmsfkit in published work.