:orphan:

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

This gallery contains example scripts demonstrating how to use atomworks for structure parsing, visualization, and analysis.

Each example is fully annotated and can be run interactively.

Enjoy exploring!


.. raw:: html

    <div class="sphx-glr-thumbnails">

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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use the atomworks.io package to load, inspect, and manipulate mmCIF structure files. You&#x27;ll see how to parse a structure, visualize it, and perform basic analysis.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_basics_thumb.svg
    :alt:

  :ref:`sphx_glr_auto_examples_basics.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Structure Manipulation Basics</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to load protein structures from various formats and explore their content using AtomWorks.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_load_and_visualize_structures_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_load_and_visualize_structures.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Loading and Visualizing Protein Structures</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to work with datasets in AtomWorks, from simple file-based datasets to complex tabular datasets with custom loaders and transform pipelines.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_dataset_exploration_thumb.svg
    :alt:

  :ref:`sphx_glr_auto_examples_dataset_exploration.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Dataset Exploration and Management in AtomWorks</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example walks through how to add custom annotations to AtomArrays, visualize them, and save them for later use.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_annotate_and_save_structures_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_annotate_and_save_structures.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Annotating and Saving Protein Structures</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to create custom Transform classes in AtomWorks using ligand pocket identification as an example. We&#x27;ll build two transforms that follow AtomWorks conventions.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_pocket_conditioning_transform_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_pocket_conditioning_transform.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Creating Custom Transforms: Ligand Pocket Conditioning</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/basics
   /auto_examples/load_and_visualize_structures
   /auto_examples/dataset_exploration
   /auto_examples/annotate_and_save_structures
   /auto_examples/pocket_conditioning_transform


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  .. container:: sphx-glr-footer sphx-glr-footer-gallery

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_