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/)
.. raw:: html
<div class="row">
.. raw:: html
</div>
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
==========================================================
[|Build Status|] (https://travis-ci.org/msmexplorer/msmexplorer)
|Coverage Status| [|License|] (https://opensource.org/licenses/MIT)
[|Documentation|] (http://msmbuilder.org/msmexplorer/)
.. raw:: html
<div class="row">
.. raw:: html
</div>
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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