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start-description\n\n**A Python toolkit for the analysis of lipid membrane simulations**\n\n.. start-badges\n\n|mdanalysis|\n|conda|\n|pypi|\n|docs|\n|actions|\n|codecov|\n|supported-versions|\n|binder|\n\n.. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16\u0026logo=data:image/x-icon;base64,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\n    :alt: Powered by MDAnalysis\n    :target: https://www.mdanalysis.org\n\n.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/lipyphilic.svg\n    :alt: Conda-fogre latest release\n    :target: https://anaconda.org/conda-forge/lipyphilic\n\n.. |pypi| image:: https://img.shields.io/pypi/v/lipyphilic.svg\n    :alt: PyPI Package latest release\n    :target: https://pypi.org/project/lipyphilic\n\n.. |docs| image:: https://readthedocs.org/projects/lipyphilic/badge/?style=flat\n    :target: https://readthedocs.org/projects/lipyphilic\n    :alt: Documentation Status\n\n.. |actions| image:: https://github.com/p-j-smith/lipyphilic/actions/workflows/tests.yml/badge.svg\n    :alt: GitHub Actions CI Status\n    :target: https://github.com/p-j-smith/lipyphilic/actions\n\n.. |codecov| image:: https://codecov.io/gh/p-j-smith/lipyphilic/branch/main/graphs/badge.svg?branch=main\n    :alt: Coverage Status\n    :target: https://codecov.io/github/p-j-smith/lipyphilic\n\n.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/lipyphilic.svg\n    :alt: Supported versions\n    :target: https://pypi.org/project/lipyphilic\n\n.. |binder| image:: https://mybinder.org/badge_logo.svg\n :target: https://mybinder.org/v2/gh/p-j-smith/lipyphilic-tutorials/main?filepath=notebooks%2F1-Introduction.ipynb\n\n.. end-badges\n\n**lipyphilic** is free software licensed under the GNU General Public License v2 or later (GPLv2+)\n\nOverview\n========\n\n**lipyphilic** is a set of tools for analysing MD simulations of lipid bilayers. It is an object-oriented\nPython package built directly on top of `MDAnalysis \u003chttps://www.mdanalysis.org/\u003e`__, and makes use of\n`NumPy \u003chttps://numpy.org/\u003e`__ and `SciPy \u003chttps://www.scipy.org/\u003e`__  for efficient computation.\nThe analysis classes are designed with the same interface as those of MDAnalysis - so if you know how to\n`use analysis modules in MDAnalysis\n\u003chttps://userguide.mdanalysis.org/stable/examples/quickstart.html#Analysis\u003e`__ then learning **lipyphilic**\nwill be a breeze.\n\nAnalysis tools in **lipyphilic** include: identifying sterol flip-flop events, calculating domain registration over time,\nand calculating local lipid compositions. **lipyphilic** also has an on-the-fly trajectory transformation to fix\nmembranes split across periodic boundaries.\n\nThese tools position **lipyphilic** as complementary to, rather than competing against, existing membrane analysis\nsoftware such as `MemSurfer \u003chttps://github.com/LLNL/MemSurfer\u003e`__ and `FatSlim \u003chttp://fatslim.github.io/\u003e`__.\n\nInteractive tutorials\n=====================\n\n.. image:: https://mybinder.org/badge_logo.svg\n :target: https://mybinder.org/v2/gh/p-j-smith/lipyphilic-tutorials/main?filepath=notebooks%2F1-Introduction.ipynb\n\nWe recommend new users take a look out our interactive tutorials. These will show you how to get the most out of **lipyphilic**\n\nBasic Usage\n===========\n\nAlternatively, check out the `Basic Usage \u003chttps://lipyphilic.readthedocs.io/en/stable/usage.html\u003e`__ example to see how to use\n**lipyphilic**, and see the `Analysis tools \u003chttps://lipyphilic.readthedocs.io/en/stable/reference/analyses.html\u003e`__\nsection for detailed information and examples on each tool.\n\nInstallation\n============\n\nThe easiest way to install **lipyphilic** along with its dependencies is through `Conda\n\u003chttps://docs.conda.io/en/latest/index.html\u003e`__::\n\n    conda config --add channels conda-forge\n    conda install lipyphilic\n\nSee the `installation guide \u003chttps://lipyphilic.readthedocs.io/en/stable/installation.html\u003e`__ for futher information.\n\nCiting\n======\n\nIf you use **lipyphilic** in your research, please cite our paper: ::\n\n    @article{LiPyphilic2021,\n        author = {Smith, Paul and Lorenz, Christian D.},\n        title = {LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations},\n        journal = {Journal of Chemical Theory and Computation},\n        year = {2021},\n        volume = {17},\n        number = {9},\n        pages = {5907-5919},\n        doi = {10.1021/acs.jctc.1c00447}\n    }\n\nPlease also cite `MDAnalysis \u003chttps://www.mdanalysis.org/pages/citations/\u003e`__, on which **lipyphilic** is built.\nIf you use the Area Per Lipid tool please also cite `Freud \u003chttps://freud.readthedocs.io/en/stable/reference/citing.html\u003e`__.\n\n.. end-description\n\nFull documentation\n==================\n\nHead to `lipyphilic.readthedocs.io \u003chttps://lipyphilic.readthedocs.io/en/stable/\u003e`__, where you will find the full\ndocumentation of **lipyphilic**'s API as well as examples of how to use the analysis tools.\n\nAcknowledgement\n===============\n\nThe respository structure and configuration of **lipyphilic** was initially based on the\n`PyLibrary Cookeicutter template \u003chttps://github.com/ionelmc/cookiecutter-pylibrary\u003e`__.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fp-j-smith%2Flipyphilic","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fp-j-smith%2Flipyphilic","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fp-j-smith%2Flipyphilic/lists"}