========
Analysis
========

.. versionadded:: 0.8.0

The :mod:`mdpow.analysis` module contains tools for analyzing whole
sets (ensembles) of FEP simulations and a framework to write new
analysis tools [Lescoulie2021]_.

.. _tools:

Analysis tools
--------------

MDPOW analysis tools are based on the :ref:`framework`. They generally
take as an input the top level directory of a complete FEP run and
then collect individual simulations and run a specific analysis over
all FEP simulations. They then make data available (typically, as a
:class:`pandas.DataFrame`).

.. toctree::
   :maxdepth: 2

   analysis/solvation
   analysis/dihedral

.. _framework:   

Ensemble Analysis Framework
---------------------------

The *Ensemble Analysis framework* [Lescoulie2021]_ allows for the
construction analysis tools that work with whole sets (ensembles) of
FEP simulations. They generally follow (and can use) standard
MDAnalysis analysis classes.

The :ref:`ensemble-objects` and :ref:`ensembleanalysis-base` sections
assume a basic understanding of object oriented programming in Python
and are for users who wish to construct their own analyses. The code
in the :ref:`tools` serves as example implementations and is described
in more detail in [Lescoulie2021]_.

.. toctree::
   :maxdepth: 1

   analysis/ensemble_analysis
   analysis/ensemble

References
----------
.. [Lescoulie2021] A. Lescoulie, "SPIDAL Summer REU 2021: Upgrading MDPOW and
		   adding analysis functionality," Technical Report, Arizona
		   State University, Tempe, AZ, 2021. doi:
		   `10.6084/m9.figshare.17156018`_

.. _`10.6084/m9.figshare.17156018`: https://doi.org/10.6084/m9.figshare.17156018