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Visualizations for statistical modelsof biomolecular dynamics.

Project description

b'MSMExplorer: data visualizations for biomolecular dynamics'
b'=========================================================='
b''
b'|Build Status| |Build status| |Coverage Status| |PyPI version| |License|'
b'|Documentation| |DOI|'
b''
b'.. raw:: html'
b''
b' <div class="row">'
b''
b'.. raw:: html'
b''
b' </div>'
b''
b'MSMExplorer is a Python visualization library for statistical models of'
b'biomolecular dynamics. It provides a high-level interface for drawing'
b'attractive statistical graphics with'
b'`MSMBuilder <http://msmbuilder.org>`__.'
b''
b'Documentation'
b'-------------'
b''
b'Online documentation is available'
b'`here <http://msmbuilder.org/msmexplorer/>`__. It includes IPython'
b'notebooks, detailed API documentation, and other useful info.'
b''
b'There are docs for the development version'
b'`here <http://msmbuilder.org/msmexplorer/development>`__. These should'
b'correspond with the github master branch.'
b''
b'Examples'
b'--------'
b''
b'.. code:: python'
b''
b' from msmbuilder.example_datasets import FsPeptide'
b' from msmbuilder.featurizer import RMSDFeaturizer'
b''
b' import msmexplorer as msme'
b''
b' # Load Fs Peptide Data'
b' traj = FsPeptide().get().trajectories[0]'
b''
b' # Calculate RMSD'
b' featurizer = RMSDFeaturizer(reference_traj=traj[0])'
b' rmsd = featurizer.partial_transform(traj).flatten()'
b''
b' # Plot Trace'
b" msme.plot_trace(rmsd, label='traj0', xlabel='Timestep', ylabel='RMSD (nm)')"
b''
b'.. figure:: http://msmbuilder.org/msmexplorer/development/_images/plot_trace.png'
b' :alt: '
b''
b'The documentation has an `example'
b'gallery <http://msmbuilder.org/msmexplorer/development/examples/>`__'
b'with short scripts showing how to use different parts of the package.'
b''
b'Dependencies'
b'------------'
b''
b'- Python 3.4+'
b''
b'Mandatory'
b'~~~~~~~~~'
b''
b'The latest versions of the following packages are required:'
b''
b'- `numpy <http://www.numpy.org/>`__'
b''
b'- `scipy <http://www.scipy.org/>`__'
b''
b'- `matplotlib <matplotlib.sourceforge.net>`__'
b''
b'- `networkx <https://networkx.github.io/>`__'
b''
b'- `pandas <http://pandas.pydata.org/>`__'
b''
b'- `seaborn <https://stanford.edu/~mwaskom/software/seaborn/>`__'
b''
b'- `statsmodels <http://statsmodels.sourceforge.net/devel/>`__'
b''
b'- `corner <http://corner.readthedocs.io/en/latest/>`__'
b''
b'- `mdtraj <https://mdtraj.org/>`__'
b''
b'- `msmbuilder <https://msmbuilder.org>`__'
b''
b'Installation'
b'------------'
b''
b'The preferred installation mechanism for ``msmexplorer`` is with'
b'``conda``:'
b''
b'.. code:: bash'
b''
b' $ conda install -c omnia msmexplorer'
b''
b"If you don't have conda, or are new to scientific python, we recommend"
b'that you download the `Anaconda scientific python'
b'distribution <https://store.continuum.io/cshop/anaconda/>`__.'
b''
b'To install from PyPI, just do:'
b''
b'::'
b''
b' pip install msmexplorer'
b''
b'You may instead want to use the development version from Github, by'
b'running'
b''
b'::'
b''
b' pip install git+git://github.com/msmexplorer/msmexplorer.git#egg=msmexplorer'
b''
b'Development'
b'-----------'
b''
b'All development happens here, on'
b'`Github <https://github.com/msmexplorer/msmexplorer>`__.'
b''
b"If you're interested in contributing to MSMExplorer, please refer to our"
b'`Contributing <http://msmbuilder.org/msmexplorer/development/contributing.html>`__'
b'guide.'
b''
b'Support'
b'-------'
b''
b'Please'
b'`submit <https://github.com/msmexplorer/msmexplorer/issues/new>`__ any'
b'bugs or questions to the Github issue tracker.'
b''
b'License'
b'-------'
b''
b'Released under a MIT license'
b''
b'Citing'
b'------'
b''
b'.. code:: bibtex'
b''
b' @misc{msmexplorer,'
b" author = {Hern{\\'{a}}ndez, Carlos and"
b' Harrigan, Matthew and'
b' Pande, Vijay},'
b' title = {msmexplorer/msmexplorer: MSMExplorer 0.3},'
b' month = oct,'
b' year = 2016,'
b' doi = {10.5281/zenodo.162942},'
b' url = {https://doi.org/10.5281/zenodo.162942}'
b' }'
b''
b'.. |Build Status| image:: https://travis-ci.org/msmexplorer/msmexplorer.svg?branch=master'
b' :target: https://travis-ci.org/msmexplorer/msmexplorer'
b'.. |Build status| image:: https://ci.appveyor.com/api/projects/status/038hirce0vlx2847?svg=true'
b' :target: https://ci.appveyor.com/project/cxhernandez/msmexplorer'
b'.. |Coverage Status| image:: https://coveralls.io/repos/github/msmexplorer/msmexplorer/badge.svg?branch=master'
b' :target: https://coveralls.io/github/msmexplorer/msmexplorer?branch=master'
b'.. |PyPI version| image:: https://badge.fury.io/py/msmexplorer.svg'
b' :target: http://badge.fury.io/py/msmexplorer'
b'.. |License| image:: https://img.shields.io/badge/license-MIT-red.svg?style=flat'
b' :target: https://opensource.org/licenses/MIT'
b'.. |Documentation| image:: https://img.shields.io/badge/docs-latest-blue.svg?style=flat'
b' :target: http://msmbuilder.org/msmexplorer/'
b'.. |DOI| image:: https://zenodo.org/badge/47228682.svg'
b' :target: https://zenodo.org/badge/latestdoi/47228682'
b''

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