========
Examples
========

|binder|

MDAnalysis maintains a collection of Jupyter notebooks as examples
of what the code can do. Each notebook can be downloaded from
`GitHub`_ to run on your own computer, or viewed as an
online tutorial on the user guide. You can also interact with
each notebook on `Binder`_.


.. toctree::
   :maxdepth: 1
   :caption: General

   quickstart
   constructing_universe
   transformations/README
   other/README

.. toctree::
   :maxdepth: 2
   :caption: Analysis

   analysis/alignment_and_rms/README
   analysis/distances_and_contacts/README
   analysis/trajectory_similarity/README
   analysis/structure/README
   analysis/reduced_dimensions/README
   analysis/polymers_and_membranes/README
   analysis/volumetric/README
   
.. |binder| image:: https://mybinder.org/badge_logo.svg
   :alt: Binder
   :target: https://mybinder.org/v2/gh/MDAnalysis/binder-env-userguide/main?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252FMDAnalysis%252FUserGuide%26urlpath%3Dtree%252FUserGuide%252Fdoc%252Fsource%252Fexamples%26branch%3Dmaster

.. _Binder: https://mybinder.org/v2/gh/MDAnalysis/binder-env-userguide/main?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252FMDAnalysis%252FUserGuide%26urlpath%3Dtree%252FUserGuide%252Fdoc%252Fsource%252Fexamples%26branch%3Dmaster
.. _GitHub: https://github.com/MDAnalysis/UserGuide/tree/master/doc/source/examples