lipyds

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

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.

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