.. |contactslogo| image:: _static/img/contacts_icon.png
   :alt: protein contacts
   :width: 100
   :align: middle

.. |GetContacts| raw:: html

   <a href="https://getcontacts.github.io" target="_blank">GetContacts</a>

.. |GetContacts_github| raw:: html

   <a href="https://github.com/getcontacts/getcontacts" target="_blank">GitHub page</a>

.. |config_file| raw:: html

   <a href="test" target="_blank">config_g2v.yml</a>

.. |github_netmd| raw:: html

   <a href="https://github.com/mazzalab/NetMD" target="_blank">NetMD's GitHub page</a>

.. |SuMD_ref| raw:: html

   <a href="https://doi.org/10.1007/978-1-4939-8630-9_17" target="_blank">1</a>

.. |dtw_ref| raw:: html

   <a href="https://tslearn.readthedocs.io/en/stable/user_guide/dtw.html" target="_blank">2</a>

.. |light_check| image:: _static/img/black_check.png
   :align: middle
   :class: only-light
   :width: 35

.. |dark_check| image:: _static/img/white_check.png 
   :align: middle
   :class: only-dark
   :width: 35

.. |notebook| raw:: html
    
    <a href="https://github.com/mazzalab/NetMD/blob/main/tutorial/netmd_notebook.ipynb" target="_blank">Notebook</a>

.. _quickstart_notebook:


Quickstart with Notebook
=========================

.. raw:: html

   <hr class="text-linebreak">

To help you get started with **NetMD**, we provide a Jupyter |notebook| that covers the following steps:

- Data preparation  
- Embedding generation  
- Analysis of molecular dynamics (MD) trajectories  

This notebook is designed to be an accessible starting point for experimenting with NetMD. It is fully editable, so you can adapt it to your own MD datasets and research questions.

You can find the example notebook in the `tutorial/` folder of the |github_netmd|.