https://github.com/p-j-smith/lipyphilic

A Python toolkit for the analyis of lipid membrane simulations

https://github.com/p-j-smith/lipyphilic

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A Python toolkit for the analyis of lipid membrane simulations

README.rst

==========
LiPyphilic
==========

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**A Python toolkit for the analysis of lipid membrane simulations**

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|mdanalysis|
|conda|
|pypi|
|docs|
|actions|
|codecov|
|supported-versions|
|binder|

.. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
    :alt: Powered by MDAnalysis
    :target: https://www.mdanalysis.org

.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/lipyphilic.svg
    :alt: Conda-fogre latest release
    :target: https://anaconda.org/conda-forge/lipyphilic

.. |pypi| image:: https://img.shields.io/pypi/v/lipyphilic.svg
    :alt: PyPI Package latest release
    :target: https://pypi.org/project/lipyphilic

.. |docs| image:: https://readthedocs.org/projects/lipyphilic/badge/?style=flat
    :target: https://readthedocs.org/projects/lipyphilic
    :alt: Documentation Status

.. |actions| image:: https://github.com/p-j-smith/lipyphilic/actions/workflows/tests.yml/badge.svg
    :alt: GitHub Actions CI Status
    :target: https://github.com/p-j-smith/lipyphilic/actions

.. |codecov| image:: https://codecov.io/gh/p-j-smith/lipyphilic/branch/main/graphs/badge.svg?branch=main
    :alt: Coverage Status
    :target: https://codecov.io/github/p-j-smith/lipyphilic

.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/lipyphilic.svg
    :alt: Supported versions
    :target: https://pypi.org/project/lipyphilic

.. |binder| image:: https://mybinder.org/badge_logo.svg
 :target: https://mybinder.org/v2/gh/p-j-smith/lipyphilic-tutorials/main?filepath=notebooks%2F1-Introduction.ipynb

.. end-badges

**lipyphilic** is free software licensed under the GNU General Public License v2 or later (GPLv2+)

Overview
========

**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 an on-the-fly trajectory transformation to fix
membranes split across periodic boundaries.

These tools position **lipyphilic** as complementary to, rather than competing against, existing membrane analysis
software such as `MemSurfer `__ and `FatSlim `__.

Interactive tutorials
=====================

.. image:: https://mybinder.org/badge_logo.svg
 :target: https://mybinder.org/v2/gh/p-j-smith/lipyphilic-tutorials/main?filepath=notebooks%2F1-Introduction.ipynb

We recommend new users take a look out our interactive tutorials. These will show you how to get the most out of **lipyphilic**

Basic Usage
===========

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.

Installation
============

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.

Citing
======

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 `__.

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Full documentation
==================

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.

Acknowledgement
===============

The respository structure and configuration of **lipyphilic** was initially based on the
`PyLibrary Cookeicutter template `__.

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