.. _documentation:

Modules
=============
Adaptivemastermsm is a Python package that is divided in three main subpackages. 
This way of structuring the code derives from the three main types of 
objects that are constructed. First, there is system, which 
result in objects of the ``System`` class; second, command execution
is managed by launcher, which come in the form of instances of the ``Launcher``
class; finally, MD data is analyzed by another objects, which are contained
in the ``Analyzer`` class. In order to coordinate these modules and enable
the implementation of the adaptive sampling algorithm, ``Controller`` class
is put on top of everything.



CONTROLLER module
-----------------
.. currentmodule:: adaptivemastermsm

.. autosummary::
    :toctree:

    controller


SYSTEM module
-------------
.. currentmodule:: adaptivemastermsm

.. autosummary::
    :toctree: 

    system


LAUNCHER module
---------------
.. currentmodule:: adaptivemastermsm

.. autosummary::
    :toctree:

    launcher


ANALYZER module
---------------
.. currentmodule:: adaptivemastermsm

.. autosummary::
    :toctree:

    analyzer
    
Examples
--------
We have put together a few simple Python notebooks to help you learn the basics
of the AdaptiveMasterMSM package. They are based on data derived from either model
systems or from molecular dynamics simulations of some simple (albeit realistic)
biomolecules. You can find the notebooks in the following 
`link <https://github.com/BioKT/AdaptiveMasterMSM/tree/develop/examples>`_.