.. _msmbuilder:

MSMBuilder
==========


.. raw:: html

    <h2 style="margin-top: -1em; font-size: 120%;">
    Statistical models for Biomolecular Dynamics</h2>

MSMBuilder is an application and python library. It builds
statistical models for high-dimensional time-series. The particular focus
of the package is on the analysis of atomistic simulations of biomolecular
dynamics such as protein folding and conformational change.

To get started via `Anaconda Python <https://www.continuum.io/downloads>`_,
use::

    conda install -c omnia msmbuilder

MSMBuilder includes algorithms for constructing dynamical models:

- :ref:`featurization`
- :ref:`decomposition`
- :ref:`cluster`
- :ref:`msm`
- :ref:`hmm`
- :ref:`ratematrix`

As well as methods for analysis and validation of the models:

- :ref:`gmrq`
- :ref:`tpt`

New users should check out:

- :ref:`background`
- :ref:`installation`
- :ref:`examples`
- :ref:`faq`

MSMBuilder is most effective as a library. Intermediate users should
familiarize themselves with:

- :ref:`apipatterns`
- :ref:`persistence`
- :ref:`changelog`


MSMBuilder is developed by primarily by researchers at Stanford University,
and we welcome contributions. The development all takes place on `Github
<https://github.com/msmbuilder/msmbuilder>`_.  MSMBuilder is licensed under
the GNU LGPL (v2.1 or later).



.. toctree::
    :maxdepth: 2
    :hidden:

    background
    installation
    examples/index
    featurization
    decomposition
    cluster
    msm
    gmrq
    tpt
    ratematrix
    hmm
    persistence
    apipatterns
    plugins
    faq
    changelog    

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