I am currently working on a 1.0 release of lipyphilic and there will be a lot of breaking changes to the API. This is because many of the modules will be moved from lipyphilic.lib to a new location lipyphilic.analysis.
However, the interface for classes / functions will mostly be unchanged and so you should be able to use them as before after changing your imports.
The flip-flop tool will be removed due to a fundamental issue with the current algorithm.
Most of the other changes will be to internal code or modernising the packaging and testing side of things.
A Python toolkit for the analysis of lipid membrane simulations
lipyphilic is free software licensed under the GNU General Public License v2 or later (GPLv2+)
lipyphilic is a set of tools for analysing MD simulations of lipid bilayers. It is an object-oriented Python package built directly on top of MDAnalysis, and makes use of NumPy and SciPy for efficient computation. The analysis classes are designed with the same interface as those of MDAnalysis - so if you know how to use analysis modules in MDAnalysis then learning lipyphilic will be a breeze.
Analysis tools in lipyphilic include: identifying sterol flip-flop events, calculating domain registration over time, and calculating local lipid compositions. lipyphilic also has three on-the-fly trajectory transformations to i) fix membranes split across periodic boundaries and ii) perform nojump coordinate unwrapping and iii) convert triclinic coordinates to their orthorhombic representation.
These tools position lipyphilic as complementary to, rather than competing against, existing membrane analysis software such as MemSurfer and FatSlim.
We recommend new users take a look out our interactive tutorials. These will show you how to get the most out of lipyphilic
Alternatively, check out the Basic Usage example to see how to use lipyphilic, and see the Analysis tools section for detailed information and examples on each tool.
The easiest way to install lipyphilic along with its dependencies is through Conda:
conda config --add channels conda-forge conda install lipyphilic
See the installation guide for futher information.
If you use lipyphilic in your research, please cite our paper:
@article{LiPyphilic2021,
author = {Smith, Paul and Lorenz, Christian D.},
title = {LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations},
journal = {Journal of Chemical Theory and Computation},
year = {2021},
volume = {17},
number = {9},
pages = {5907-5919},
doi = {10.1021/acs.jctc.1c00447}
}
Please also cite MDAnalysis, on which lipyphilic is built. If you use the Area Per Lipid tool please also cite Freud.
Head to lipyphilic.readthedocs.io, where you will find the full documentation of lipyphilic's API as well as examples of how to use the analysis tools.
The respository structure and configuration of lipyphilic was initially based on the PyLibrary Cookeicutter template.