| Name | lipyphilic JSON |
| Version |
0.11.0
JSON |
| download |
| home_page | |
| Summary | Analyse MD simulations of lipids with python' |
| upload_time | 2023-11-30 10:25:35 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.10 |
| license | |
| keywords |
lipid
molecular dynamics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
==========
LiPyphilic
==========
.. start-description
**A Python toolkit for the analysis of lipid membrane simulations**
.. start-badges
|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/ci.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 <https://www.mdanalysis.org/>`__, and makes use of
`NumPy <https://numpy.org/>`__ and `SciPy <https://www.scipy.org/>`__ 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
<https://userguide.mdanalysis.org/stable/examples/quickstart.html#Analysis>`__ 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 <https://github.com/LLNL/MemSurfer>`__ and `FatSlim <http://fatslim.github.io/>`__.
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 <https://lipyphilic.readthedocs.io/en/stable/usage.html>`__ example to see how to use
**lipyphilic**, and see the `Analysis tools <https://lipyphilic.readthedocs.io/en/stable/reference/analyses.html>`__
section for detailed information and examples on each tool.
Installation
============
The easiest way to install **lipyphilic** along with its dependencies is through `Conda
<https://docs.conda.io/en/latest/index.html>`__::
conda config --add channels conda-forge
conda install lipyphilic
See the `installation guide <https://lipyphilic.readthedocs.io/en/stable/installation.html>`__ 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 <https://www.mdanalysis.org/pages/citations/>`__, on which **lipyphilic** is built.
If you use the Area Per Lipid tool please also cite `Freud <https://freud.readthedocs.io/en/stable/reference/citing.html>`__.
.. end-description
Full documentation
==================
Head to `lipyphilic.readthedocs.io <https://lipyphilic.readthedocs.io/en/stable/>`__, 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 <https://github.com/ionelmc/cookiecutter-pylibrary>`__.
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It is an object-oriented\nPython package built directly on top of `MDAnalysis <https://www.mdanalysis.org/>`__, and makes use of\n`NumPy <https://numpy.org/>`__ and `SciPy <https://www.scipy.org/>`__ 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<https://userguide.mdanalysis.org/stable/examples/quickstart.html#Analysis>`__ 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 <https://github.com/LLNL/MemSurfer>`__ and `FatSlim <http://fatslim.github.io/>`__.\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. 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