Examples
========

This page provides a series of examples, tutorials and recipes to help you
get started with ``mdtraj``.

Each subsection is a notebook.  To open these notebooks in a "live"
Jupyter/IPython session and execute the documentation interactively, you
need to download the repository and start the Jupyter notebook.

If you installed `MDTraj` from source, you will need to navigate to
:code:`path-to-mdtraj/examples`. The notebook files for these examples and
the notebooks are available in the top level  `examples folder
<https://github.com/mdtraj/mdtraj/tree/master/examples>`_ on github too. In
the directory with the notebook files, start an IPython notebook server:

.. code:: bash

   $ jupyter notebook

.. warning:: The pre-filled out notebooks are far less fun than running them
             yourself!

.. toctree::
   :maxdepth: 1

   introduction
   atom-selection
   centroids
   clustering
   hbonds
   pi_stacking
   iterload
   native-contact
   openmm
   pca
   ramachandran-plot
   rmsd-benchmark
   rmsd-drift
   solvent-accessible-surface-area
   two-pass-clustering


Let us know if you would like to contribute other example notebooks, or
have any suggestions for how these can be improved.

