Metadata-Version: 2.1
Name: ENPMDA
Version: 0.4.0
Summary: parallel analysis for ensemble simulations
Home-page: https://github.com/yuxuanzhuang/ENPMDA
Author: Yuxuan Zhuang
Author-email: yuxuan.zhuang@dbb.su.se
License: GNU General Public License v3
Keywords: ENPMDA
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
License-File: LICENSE
License-File: AUTHORS.rst

============================
Ensemble Parallel MDAnalysis
============================

|mdanalysis|

.. |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
    
.. image:: https://img.shields.io/pypi/v/ENPMDA.svg
        :target: https://pypi.python.org/pypi/ENPMDA

.. image:: https://img.shields.io/travis/yuxuanzhuang/ENPMDA.svg
        :target: https://travis-ci.com/yuxuanzhuang/ENPMDA

.. image:: https://readthedocs.org/projects/ENPMDA/badge/?version=latest
        :target: https://ENPMDA.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

.. image:: https://codecov.io/gh/yuxuanzhuang/ENPMDA/branch/main/graph/badge.svg
        :alt: Coverage Status
        :target: https://codecov.io/gh/yuxuanzhuang/ENPMDA

.. image:: https://colab.research.google.com/assets/colab-badge.svg
        :alt: Open in colab
        :target: https://colab.research.google.com/github/yuxuanzhuang/ENPMDA/blob/main/docs/source/examples/examples.ipynb

Warning
-------

This is still under constrution.

ENPMDA
------

Parallel analysis for ensemble simulations
powered by MDAnalysis.
ENPMDA stores metadata in ``pandas.DataFrame``
and distributes computation jobs in ``dask.DataFrame``
so that the parallel analysis can be performed
not only for one single trajectory
but also across simulations and analyses.

It can be used as an initial inspection of
the raw trajectories as well as a framework for 
extracting features from final production simulations
for further e.g. machine learning and markov
state modeling. It automatically fixes the PBC issue and
align and center the protein inside the simulation box.
It also works for multimeric proteins!

The framework is intended to be adaptable by being able to
simply wrapping MDAnalysis analysis functions without worrying
about the parallel machinery behind.


* Free software: GNU General Public License v3
* Documentation: https://ENPMDA.readthedocs.io.


Features
--------

* Parallel analysis for ensemble simulations.
* Dataframe for storing and accessing results.
* dask-based task scheduler, suitable for both workstations and clusters.
* Expandable analysis library powered by MDAnalysis.


Workflow Illustration
---------------------
.. image:: /docs/source/_static/example.png
  :width: 700
  :alt: Illustration of the ensemble analysis workflow.


TODO
----

* more analysis functions.
* unit testing
* benchmarking
* option to retrieve numerical results 
* documentation
* add functions to cancel running tasks


Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage



=======
History
=======

0.1.0 (2022-05-09)
------------------

* First release on PyPI.
