Metadata-Version: 1.2
Name: lipyphilic
Version: 0.6.3
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/>`__ 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 two on-the-fly trajectory transformations to i) fix
        membranes split across periodic boundaries and ii) perform nojump coordinate unwrapping. 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 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
        ====================
        
        0.6.3 (2021-05-09)
        ------------------
        * PR#60 AssignLeaflets and AssignCurvedLeaflets inherit from shared leaflet analysis base class
        * PR#59 Ensure SCC.weighted_average can handle different sized sn1 and sn2 residue groups.
        * PR#56 Update docs
        
        0.6.2 (2021-04-18)
        ------------------
        * PR#54 Fixed typos in docs 
        * PR#53 Improved performance of lipyphilic.lib.flip_flop.FlipFlop
        * PR#52 Improved performance of lipyphilic.lib.neighbours.Neighbours (Fixes #51)
        
        0.6.1 (2021-04-16)
        ------------------
        * PR#49 Add min_diff argument to transformations.center_membrane
        * PR#48 Add MDAnalysis badge to README and fix typos in the docs
        * PR#47 Fixed typos in docs 
        
        0.6.0 (2021-03-26)
        ------------------
        * PR#44 Refactor the Registration analysis to have a more useful API
        * PR#43 Add a method for calculating the lipid enrichment/depletion index
        * PR#42 Add a MSD and lateral diffusion analysis, as well as a transformation to perform "nojump" unwrapping.
        * PR#39 Add support for assigning lipids to leaflets of highly curved membranes
        
        0.5.0 (2021-03-16)
        ------------------
        * PR#38 Add a trajectory transformation for unwrapping broken membranes (Fixes #37)
        * PR#36 Add method for projecting areas onto the membrane plane (Fixes #33)
        * PR#35 Added a tool for calculating membrane thickness (Fixes #34)
        * PR#32 ZThickness.average() now returns a new ZThickness object rather than a NumPy array
        * PR#31 SCC.weighted_average() now returns a new SCC object rather than a NumPy array
        * PR#30 Add class for plotting projections of membrane properties onto the xy plane.
        * PR#29 Added plotting of joint probability distributions or PMFs (Fixed #28).
        
        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
