https://github.com/lilyminium/lipyds

https://github.com/lilyminium/lipyds

Last synced: 2 months ago
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• Host: GitHub
• URL: https://github.com/lilyminium/lipyds
• Owner: lilyminium
• License: lgpl-3.0
• Created: 2021-04-25T23:05:19.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2024-09-23T14:41:39.000Z (9 months ago)
• Last Synced: 2024-10-16T11:57:45.343Z (8 months ago)
• Language: Python
• Size: 58.1 MB
• Stars: 6
• Watchers: 3
• Forks: 7
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md
  • Dei: docs/dei.rst

Awesome Lists containing this project

README

        
lipyds

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

[//]: # (Badges)

[![GitHub Actions Build Status](https://github.com/lilyminium/lipyds/workflows/CI/badge.svg)](https://github.com/lilyminium/lipyds/actions?query=workflow%3ACI)

[![codecov](https://codecov.io/gh/lilyminium/lipyds/branch/master/graph/badge.svg)](https://codecov.io/gh/lilyminium/lipyds/branch/master)

[![Documentation Status](https://readthedocs.org/projects/lipyds/badge/?version=latest)](https://lipyds.readthedocs.io/en/latest/?badge=latest)

[![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 toolkit for leaflet-based membrane analysis

**Note: this code was used for a publication requiring membrane analysis.

It is still in early development status and should be regarded as experimental --

the API is very likely to change in the future. Please use at your own risk!**

**Note: this package is temporarily stripped back to just supporting the LeafletFinder

to unblock core MDAnalysis development.**

The initial code was first used in the below publication. Please cite it if

you use this package:

Wilson, K. A.; Wang, L.; Lin, Y. C.; O’Mara, M. L.

Investigating the Lipid Fingerprint of SLC6 Neurotransmitter Transporters:

A Comparison of DDAT, HDAT, HSERT, and GlyT2. BBA Advances 2021, 1, 100010.

doi: [10.1016/j.bbadva.2021.100010](https://doi.org/10.1016/j.bbadva.2021.100010)

The package is built on MDAnalysis. Please cite its two papers if you use this

package:

N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,

and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics

Simulations. *J. Comput. Chem.* **32** (2011),

2319–2327. doi:10.1002/jcc.21787.

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.

## Installation

A release will be forthcoming. Until then, you can build this from source.

```python

git clone https://github.com/lilyminium/lipyds.git

conda create --name lipyds -c conda-forge cython matplotlib nptyping "numpy>=1.20.0" pandas "scikit-learn>=0.21.0" scipy

conda activate lipyds

cd lipyds

python setup.py install

```

### Copyright

Copyright (c) 2021, Lily Wang