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MSMExplorer: data visualizations for biomolecular dynamics

Project description

MSMExplorer: data visualizations for biomolecular dynamics
==========================================================

[|Build Status|] (https://travis-ci.org/msmexplorer/msmexplorer)
|Coverage Status| [|License|] (https://opensource.org/licenses/MIT)
[|Documentation|] (http://msmbuilder.org/msmexplorer/)

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MSMExplorer is a Python visualization library for statistical models of
biomolecular dynamics. It provides a high-level interface for drawing
attractive statistical graphics with
`MSMBuilder <http://msmbuilder.org>`__.

Documentation
-------------

Online documentation is available
`here <http://msmbuilder.org/msmexplorer/>`__. It includes IPython
notebooks, detailed API documentation, and other useful info.

There are docs for the development version
`here <http://msmbuilder.org/msmexplorer/development>`__. These should
more or less correspond with the github master branch, but they're not
built automatically and thus may fall out of sync at times.

Examples
--------

.. code:: python

from msmbuilder.example_datasets import FsPeptide
from msmbuilder.featurizer import RMSDFeaturizer

import msmexplorer as msme

# Load Fs Peptide Data
traj = FsPeptide().get().trajectories

# Calculate RMSD
featurizer = RMSDFeaturizer(reference_traj=traj[0][0])
rmsd = featurizer.transform(traj)

# Plot Trace
msme.plot_trace(rmsd[0].flatten(), label='traj0', xlabel='Timestep', ylabel='RMSD (nm)')

.. figure:: http://msmbuilder.org/msmexplorer/development/_images/plot_trace.png
:alt:

The documentation has an `example
gallery <http://msmbuilder.org/msmexplorer/development/examples/>`__
with short scripts showing how to use different parts of the package.

Dependencies
------------

- Python 3.4+

Mandatory
~~~~~~~~~

- `numpy <http://www.numpy.org/>`__

- `scipy <http://www.scipy.org/>`__

- `matplotlib <matplotlib.sourceforge.net>`__

- `networkx <https://networkx.github.io/>`__

- `pandas <http://pandas.pydata.org/>`__

- `seaborn <https://stanford.edu/~mwaskom/software/seaborn/>`__

- `statsmodels <http://statsmodels.sourceforge.net/devel/>`__

- `corner <http://corner.readthedocs.io/en/latest/>`__

- `mdtraj <https://mdtraj.org/>`__

- `msmbuilder <https://msmbuilder.org>`__

Installation
------------

The preferred installation mechanism for ``msmexplorer`` is with
``conda``:

.. code:: bash

$ conda install -c omnia msmexplorer

If you don't have conda, or are new to scientific python, we recommend
that you download the `Anaconda scientific python
distribution <https://store.continuum.io/cshop/anaconda/>`__.

To install from PyPI, just do:

::

pip install msmexplorer

You may instead want to use the development version from Github, by
running

::

pip install git+git://github.com/msmexplorer/msmexplorer.git#egg=msmexplorer

Development
-----------

https://github.com/msmexplorer/msmexplorer

Please
`submit <https://github.com/msmexplorer/msmexplorer/issues/new>`__ any
bugs you encounter to the Github issue tracker.

License
-------

Released under a MIT license

.. |Build Status| image:: https://travis-ci.org/msmexplorer/msmexplorer.svg?branch=master
.. |Coverage Status| image:: https://coveralls.io/repos/github/msmexplorer/msmexplorer/badge.svg?branch=master
:target: https://coveralls.io/github/msmexplorer/msmexplorer?branch=master
.. |License| image:: https://img.shields.io/badge/license-MIT-red.svg?style=flat
.. |Documentation| image:: https://img.shields.io/badge/docs-latest-blue.svg?style=flat

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