Metadata-Version: 1.2
Name: lipyphilic
Version: 0.4.0
Summary: Analyse MD simulations of lipids with python
Home-page: https://github.com/p-j-smith/lipyphilic
Author: Paul Smith
Author-email: paul.smith@kcl.ac.uk
License: LGPL-2.1-or-later
Project-URL: Documentation, https://lipyphilic.readthedocs.io/
Project-URL: Changelog, https://lipyphilic.readthedocs.io/en/latest/changelog.html
Project-URL: Issue Tracker, https://github.com/p-j-smith/lipyphilic/issues
Description: ==========
        LiPyphilic
        ==========
        
        .. start-description
        
        **A python toolkit for the analyis of lipid membrane simulations**
        
        
        
        **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/>`__, `SciPy <https://www.scipy.org/>`__ and `pandas <https://pandas.pydata.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 you know how
        to use **lipyphilic**!
         
        Analysis tools in **lipyphilic** include: identifying sterol flip-flop events, calculating domain registration over time,
        and calculating local lipid compositions. 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/>`__.
        
        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 exmaples 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 project, please cite `MDAnalysis <https://www.mdanalysis.org/pages/citations/>`__ and
        if you use the Area Per Lipid tool please also cite `Freud <https://freud.readthedocs.io/en/stable/reference/citing.html>`__.
        
        There is currently no paper describing **lipyphilic**, but we're working on it. In the meantime, if you like what we
        do, please tell everyone you know to check out **lipyphilic**! And if there are things you think we could improve, features
        you would like to see added, or pesky bugs you that need to be fixed, please raise an issue on
        `github <https://github.com/p-j-smith/lipyphilic/issues>`__.
        
        .. 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.
        
        Acknowlegment
        =============
        
        The respository structure of **lipyphilic** is based on the
        `PyLibrary Cookeicutter template <https://github.com/ionelmc/cookiecutter-pylibrary>`__.
        
        lipyphilic CHANGELOG
        ====================
        
        0.4.0 (2021-03-05)
        ------------------
        
        * PR#26 Added a tool to calculate the thickness of lipids or their tails (Fixes #25)
        * PR#24 Added a tool to calculate the coarse-grained order parameter (Fixes #23)
        * PR#22 Added a tool to calculate orientation of lipids in a bilayer (Fixes #20)
        * PR#21 Added a tool to calculate lipid height in a bilayer (Fixes #19)
        * Better description of analysis tools in the docs
        * Updated installation instructions, including installing via conda-forge
        
        0.3.2 (2021-02-27)
        ------------------
        
        * Fix typo in requirements
        
        0.3.1 (2021-02-27)
        ------------------
        
        * Add support for numpy 1.20
        
        0.3.0 (2021-02-26)
        ------------------
        
        * Fix neighbour calculation for non-sequential residue indices
          Fixes #11
        * Added a tool to calculate interleaflet registration
        
        0.2.0 (2021-02-23)
        ------------------
        
        * Improved documentation
        * Add method to count number of each neighbour type
        * Add functionality to find neighbouring lipids
        
        0.1.0 (2021-02-17)
        ------------------
        
        * Add functionality to find flip-flop events in bilayers
        * Add functionality to calculate area per lipid
        * Add functionality to find assign lipids to leaflets in a bilayer
        
        
        0.0.0 (2021-02-08)
        ------------------
        
        * First release on PyPI.
        
Keywords: lipids,molecular dynamics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.6
