.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_pcd.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_plot_pcd.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_plot_pcd.py:


Create and visualize a molecular point cloud
============================================

.. GENERATED FROM PYTHON SOURCE LINES 5-12

.. code-block:: Python

    from plotly.io import show

    from aidsorb.utils import pcd_from_file
    from aidsorb.visualize import draw_pcd

    # sphinx_gallery_thumbnail_number = 2








.. GENERATED FROM PYTHON SOURCE LINES 13-15

Create the point cloud
----------------------

.. GENERATED FROM PYTHON SOURCE LINES 17-24

.. code-block:: Python


    # We add electronegativity as additional feature to atomic number.
    name, pcd = pcd_from_file('IRMOF-1.xyz', features=['en_pauling'])

    print(f'The name of the point cloud is: {name}')
    print(f'The point cloud has shape: {pcd.shape}')





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    The name of the point cloud is: IRMOF-1
    The point cloud has shape: (424, 5)




.. GENERATED FROM PYTHON SOURCE LINES 25-27

Visualize it
------------

.. GENERATED FROM PYTHON SOURCE LINES 27-32

.. code-block:: Python


    fig = draw_pcd(pcd, scheme='jmol')
    fig.update_layout(margin=dict(b=0, t=0, l=0, r=0))  # Optional.
    show(fig)




.. raw:: html
    :file: images/sphx_glr_plot_pcd_001.html





.. GENERATED FROM PYTHON SOURCE LINES 33-40

.. tip::

    You can also use the CLI:

    .. code-block:: console

        $ aidsorb visualize path/to/structure

.. GENERATED FROM PYTHON SOURCE LINES 42-47

.. code-block:: Python


    # Color it by electronegativity.
    fig = draw_pcd(pcd, feature_to_color=(4, 'Electronegativity'), colorscale='viridis')
    fig.update_layout(margin=dict(b=0, t=0, l=0, r=0))  # Optional.
    show(fig)



.. raw:: html
    :file: images/sphx_glr_plot_pcd_002.html






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 10.438 seconds)


.. _sphx_glr_download_auto_examples_plot_pcd.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

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

      :download:`Download Jupyter notebook: plot_pcd.ipynb <plot_pcd.ipynb>`

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

      :download:`Download Python source code: plot_pcd.py <plot_pcd.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_pcd.zip <plot_pcd.zip>`


.. only:: html

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

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