.. _mdtraj_adapted:

Tutorials adapted from MDtraj
=============================

try ``pytraj`` online:

.. image:: http://mybinder.org/badge.svg
   :target: http://mybinder.org/repo/hainm/notebook-pytraj

.. contents::

Clustering with scipy
---------------------

Original tutorial is from `MDtraj <http://mdtraj.org/latest/examples/clustering.html>`_

.. note:: this example only shows how to populate ``pytraj`` to ``python``'s ecosystem. Users should check :ref:`clustering`

.. notebook:: data/clustering_mdtraj_adapted.ipynb
   :skip_exceptions:

Principal component analysis with sklearn
-----------------------------------------

Original tutorial is from `here <http://mdtraj.org/latest/examples/pca.html>`_

.. note:: cpptraj (then pytraj) has PCA analysis. Doc is coming soon.

.. notebook:: data/pca_mdtraj_adapted.ipynb
   :skip_exceptions: