https://github.com/mdanalysis/mdaencore
Ensemble overlap comparison software for molecular data.
https://github.com/mdanalysis/mdaencore
Last synced: 5 months ago
JSON representation
Ensemble overlap comparison software for molecular data.
- Host: GitHub
- URL: https://github.com/mdanalysis/mdaencore
- Owner: MDAnalysis
- License: gpl-2.0
- Created: 2023-07-20T20:39:10.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-11-11T09:19:10.000Z (over 1 year ago)
- Last Synced: 2025-04-03T07:24:28.343Z (about 1 year ago)
- Language: Python
- Homepage: http://www.mdanalysis.org/mdaencore/
- Size: 12.2 MB
- Stars: 0
- Watchers: 8
- Forks: 0
- Open Issues: 20
-
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
mdaencore
==============================
[//]: # (Badges)
| **Latest release** | [![Last release tag][lastreleasetag]][githubreleases] ![GitHub commits since latest release (by date) for a branch][commitssincerelease] [![Documentation Status][badge_docs]][docsurl] [![Anaconda-Server Badge][badge_condaforge]][conda_url]|
| :------ | :------- |
| **Status** | [![GH Actions Status][badge_actions]][mainworkflow] [![codecov][badge_codecov]][codecovio] |
| **Community** | [![License: GPL v2][badge_license]][licenseinfo] [![Powered by MDAnalysis][mdanalysis_badge]][mdaorg] |
[badge_actions]: https://github.com/MDAnalysis/mdaencore/actions/workflows/gh-ci.yaml/badge.svg
[badge_codecov]: https://codecov.io/gh/MDAnalysis/mdaencore/branch/main/graph/badge.svg
[badge_license]: https://img.shields.io/badge/License-GPLv2-blue.svg
[badge_docs]: https://github.com/MDAnalysis/mdaencore/actions/workflows/docs.yaml/badge.svg?branch=main
[badge_condaforge]: https://anaconda.org/conda-forge/mdaencore/badges/version.svg
[conda_url]: https://anaconda.org/conda-forge/mdaencore
[codecovio]: https://codecov.io/gh/MDAnalysis/mdaencore/branch/main
[commitssincerelease]: https://img.shields.io/github/commits-since/MDAnalysis/mdaencore/latest
[githubreleases]: https://github.com/MDAnalysis/mdaencore/releases
[lastreleasetag]: https://img.shields.io/github/release-pre/MDAnalysis/mdaencore.svg
[licenseinfo]: https://www.gnu.org/licenses/gpl-2.0
[mainworkflow]: https://github.com/MDAnalysis/mdaencore/actions?query=branch%3Amain+workflow%3Agh-ci
[mdanalysis_badge]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,AAABAAEAEBAAAAEAIAAoBAAAFgAAACgAAAAQAAAAIAAAAAEAIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJD+XwCY/fEAkf3uAJf97wGT/a+HfHaoiIWE7n9/f+6Hh4fvgICAjwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACT/yYAlP//AJ///wCg//8JjvOchXly1oaGhv+Ghob/j4+P/39/f3IAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJH8aQCY/8wAkv2kfY+elJ6al/yVlZX7iIiI8H9/f7h/f38UAAAAAAAAAAAAAAAAAAAAAAAAAAB/f38egYF/noqAebF8gYaagnx3oFpUUtZpaWr/WFhY8zo6OmT///8BAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAgICAn46Ojv+Hh4b/jouJ/4iGhfcAAADnAAAA/wAAAP8AAADIAAAAAwCj/zIAnf2VAJD/PAAAAAAAAAAAAAAAAICAgNGHh4f/gICA/4SEhP+Xl5f/AwMD/wAAAP8AAAD/AAAA/wAAAB8Aov9/ALr//wCS/Z0AAAAAAAAAAAAAAACBgYGOjo6O/4mJif+Pj4//iYmJ/wAAAOAAAAD+AAAA/wAAAP8AAABhAP7+FgCi/38Axf4fAAAAAAAAAAAAAAAAiIiID4GBgYKCgoKogoB+fYSEgZhgYGDZXl5e/m9vb/9ISEjpEBAQxw8AAFQAAAAAAAAANQAAADcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAjo6Mb5iYmP+cnJz/jY2N95CQkO4pKSn/AAAA7gAAAP0AAAD7AAAAhgAAAAEAAAAAAAAAAACL/gsAkv2uAJX/QQAAAAB9fX3egoKC/4CAgP+NjY3/c3Nz+wAAAP8AAAD/AAAA/wAAAPUAAAAcAAAAAAAAAAAAnP4NAJL9rgCR/0YAAAAAfX19w4ODg/98fHz/i4uL/4qKivwAAAD/AAAA/wAAAP8AAAD1AAAAGwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALGxsVyqqqr/mpqa/6mpqf9KSUn/AAAA5QAAAPkAAAD5AAAAhQAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADkUFBSuZ2dn/3V1df8uLi7bAAAATgBGfyQAAAA2AAAAMwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAB0AAADoAAAA/wAAAP8AAAD/AAAAWgC3/2AAnv3eAJ/+dgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA9AAAA/wAAAP8AAAD/AAAA/wAKDzEAnP3WAKn//wCS/OgAf/8MAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIQAAANwAAADtAAAA7QAAAMAAABUMAJn9gwCe/e0Aj/2LAP//AQAAAAAAAAAA
[mdaorg]: https://mdanalysis.org
[docsurl]: https://www.mdanalysis.org/mdaencore/
Ensemble overlap comparison software for molecular data.
mdaencore is bound by a [Code of Conduct](https://github.com/MDAnalysis/mdaencore/blob/main/CODE_OF_CONDUCT.md).
### Installation
To build mdaencore 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.
Install in your preferred conda environment with
```
conda install -c conda-forge mdaencore
```
To update
```
conda update -c conda-forge mdaencore
```
#### 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 -e ".[test,doc]"
```
### Copyright
The mdaencore source code is hosted at https://github.com/MDAnalysis/mdaencore
and is available under the GNU General Public License, version 2 or any later version (see the file [LICENSE](https://github.com/MDAnalysis/mdaencore/blob/main/LICENSE)).
Please note that the code is packaged and released under the terms of the [GNU General Public License, version 3](https://www.gnu.org/licenses/gpl-3.0.en.html) or any later version.
Copyright (c) 2023, mdaencore authors (see the file [AUTHORS.md](https://github.com/MDAnalysis/mdaencore/blob/release_v1.0.0/AUTHORS.md))
#### 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) and the [ENCORE paper](https://doi.org/10.1371/journal.pcbi.1004415) when using mdaencore in published work:
1. M. Tiberti, E. Papaleo, T. Bengtsen, W. Boomsma, and K. Lindorff-Larsen. ENCORE: Software for quantitative ensemble comparison. PLoS Comput Biol, 11 (2015), e1004415. doi: 10.1371/journal.pcbi.1004415
2. R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 98-105, Austin, TX, 2016. SciPy. doi:10.25080/Majora-629e541a-00e