Metadata-Version: 1.1
Name: msmexplorer
Version: 0.2.0
Summary: Visualizations for statistical modelsof biomolecular dynamics.
Home-page: https://github.com/cxhernandez/msmexplorer
Author: Carlos Xavier Hernández
Author-email: cxh@stanford.edu
License: LGPLv2+
Download-URL: https://github.com/cxhernandez/msmexplorer/tarball/master
Description: b'MSMExplorer: data visualizations for biomolecular dynamics\n==========================================================\n\n[|Build Status|] (https://travis-ci.org/msmexplorer/msmexplorer) |Build\nstatus| |Coverage Status| |PyPI version| [|License|]\n(https://opensource.org/licenses/MIT) [|Documentation|]\n(http://msmbuilder.org/msmexplorer/) |DOI|\n\n.. raw:: html\n\n   <div class="row">\n\n.. raw:: html\n\n   </div>\n\nMSMExplorer is a Python visualization library for statistical models of\nbiomolecular dynamics. It provides a high-level interface for drawing\nattractive statistical graphics with\n`MSMBuilder <http://msmbuilder.org>`__.\n\nDocumentation\n-------------\n\nOnline documentation is available\n`here <http://msmbuilder.org/msmexplorer/>`__. It includes IPython\nnotebooks, detailed API documentation, and other useful info.\n\nThere are docs for the development version\n`here <http://msmbuilder.org/msmexplorer/development>`__. These should\nmore or less correspond with the github master branch, but they\'re not\nbuilt automatically and thus may fall out of sync at times.\n\nExamples\n--------\n\n.. code:: python\n\n    from msmbuilder.example_datasets import FsPeptide\n    from msmbuilder.featurizer import RMSDFeaturizer\n\n    import msmexplorer as msme\n\n    # Load Fs Peptide Data\n    traj = FsPeptide().get().trajectories[0]\n\n    # Calculate RMSD\n    featurizer = RMSDFeaturizer(reference_traj=traj[0])\n    rmsd = featurizer.partial_transform(traj).flatten()\n\n    # Plot Trace\n    msme.plot_trace(rmsd, label=\'traj0\', xlabel=\'Timestep\', ylabel=\'RMSD (nm)\')\n\n.. figure:: http://msmbuilder.org/msmexplorer/development/_images/plot_trace.png\n   :alt: \n\nThe documentation has an `example\ngallery <http://msmbuilder.org/msmexplorer/development/examples/>`__\nwith short scripts showing how to use different parts of the package.\n\nDependencies\n------------\n\n-  Python 3.4+\n\nMandatory\n~~~~~~~~~\n\n-  `numpy <http://www.numpy.org/>`__\n\n-  `scipy <http://www.scipy.org/>`__\n\n-  `matplotlib <matplotlib.sourceforge.net>`__\n\n-  `networkx <https://networkx.github.io/>`__\n\n-  `pandas <http://pandas.pydata.org/>`__\n\n-  `seaborn <https://stanford.edu/~mwaskom/software/seaborn/>`__\n\n-  `statsmodels <http://statsmodels.sourceforge.net/devel/>`__\n\n-  `corner <http://corner.readthedocs.io/en/latest/>`__\n\n-  `mdtraj <https://mdtraj.org/>`__\n\n-  `msmbuilder <https://msmbuilder.org>`__\n\nInstallation\n------------\n\nThe preferred installation mechanism for ``msmexplorer`` is with\n``conda``:\n\n.. code:: bash\n\n    $ conda install -c omnia msmexplorer\n\nIf you don\'t have conda, or are new to scientific python, we recommend\nthat you download the `Anaconda scientific python\ndistribution <https://store.continuum.io/cshop/anaconda/>`__.\n\nTo install from PyPI, just do:\n\n::\n\n    pip install msmexplorer\n\nYou may instead want to use the development version from Github, by\nrunning\n\n::\n\n    pip install git+git://github.com/msmexplorer/msmexplorer.git#egg=msmexplorer\n\nDevelopment\n-----------\n\nhttps://github.com/msmexplorer/msmexplorer\n\nPlease\n`submit <https://github.com/msmexplorer/msmexplorer/issues/new>`__ any\nbugs you encounter to the Github issue tracker.\n\nLicense\n-------\n\nReleased under a MIT license\n\nCiting\n------\n\n.. code:: bibtex\n\n    @misc{msmexplorer,\n      author       = {Carlos X. Hern\xc3\xa1ndez  and\n                      Vijay S. Pande},\n      title        = {MSMExplorer},\n      month        = aug,\n      year         = 2016,\n      doi          = {10.5281/zenodo.61277},\n      url          = {http://dx.doi.org/10.5281/zenodo.61277}\n    }\n\n.. |Build Status| image:: https://travis-ci.org/msmexplorer/msmexplorer.svg?branch=master\n.. |Build status| image:: https://ci.appveyor.com/api/projects/status/038hirce0vlx2847?svg=true\n   :target: https://ci.appveyor.com/project/cxhernandez/msmexplorer\n.. |Coverage Status| image:: https://coveralls.io/repos/github/msmexplorer/msmexplorer/badge.svg?branch=master\n   :target: https://coveralls.io/github/msmexplorer/msmexplorer?branch=master\n.. |PyPI version| image:: https://badge.fury.io/py/msmexplorer.svg\n   :target: http://badge.fury.io/py/msmexplorer\n.. |License| image:: https://img.shields.io/badge/license-MIT-red.svg?style=flat\n.. |Documentation| image:: https://img.shields.io/badge/docs-latest-blue.svg?style=flat\n.. |DOI| image:: https://zenodo.org/badge/9890/msmexplorer/msmexplorer.svg\n   :target: https://zenodo.org/badge/latestdoi/9890/msmexplorer/msmexplorer\n'
Keywords: visualizations,biomolecular,simulations,markov state models
Platform: Windows
Platform: Linux
Platform: Mac OS-X
Platform: Unix
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Topic :: Scientific/Engineering
