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

.. only:: html

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

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

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

.. _sphx_glr_examples_gallery_structure_peoe_visualization.py:


Partial charge distribution
===========================

This examples shows how partial charges are distributed in a
small molecule.
The charges are calculated using the PEOE method
:footcite:`Gasteiger1980`.

.. footbibliography::

.. GENERATED FROM PYTHON SOURCE LINES 12-129



.. image-sg:: /examples/gallery/structure/images/sphx_glr_peoe_visualization_001.png
   :alt: peoe visualization
   :srcset: /examples/gallery/structure/images/sphx_glr_peoe_visualization_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    # Code source: Patrick Kunzmann
    # License: BSD 3 clause

    import numpy as np
    from sklearn.decomposition import PCA
    import matplotlib.pyplot as plt
    from matplotlib.colors import Normalize
    from matplotlib.cm import ScalarMappable
    import biotite.structure as struc
    import biotite.structure.info as info
    import biotite.structure.graphics as graphics


    # Acetylsalicylic acid
    MOLECULE_NAME = "AIN"

    # The number of iterations for the PEOE algorithm
    ITERATION_NUMBER = 6
    # The size of the element lables
    ELEMENT_FONT_SIZE = 10
    # The scaling factor of the atom 'balls'
    BALL_SCALE = 20
    # The higher this number, the more detailed are the rays
    N_RAY_STEPS = 20
    # The scaling factor of the 'ray' of charged molecules
    RAY_SCALE = 100
    # The transparency value for each 'ray ring'
    RAY_ALPHA = 0.03
    # The color map to use to depict the charge
    CMAP_NAME = "bwr_r"



    # Get an atom array for the selected molecule
    molecule = info.residue(MOLECULE_NAME)

    # Align molecule with principal component analysis:
    # The component with the least variance, i.e. the axis with the lowest
    # number of atoms lying over each other, is aligned to the z-axis,
    # which points into the plane of the figure
    pca = PCA(n_components=3)
    pca.fit(molecule.coord)
    molecule = struc.align_vectors(molecule, pca.components_[-1], [0, 0, 1])

    # Balls should be colored by partial charge
    charges = struc.partial_charges(molecule, ITERATION_NUMBER)
    # Later this variable stores values between 0 and 1 for use in color map
    normalized_charges = charges.copy()
    # Show no partial charge for atoms
    # that are not parametrized for the PEOE algorithm
    normalized_charges[np.isnan(normalized_charges)] = 0
    # Norm charge values to highest absolute value
    max_charge = np.max(np.abs(normalized_charges))
    normalized_charges /= max_charge
    # Transform range (-1, 1) to range (0, 1)
    normalized_charges = (normalized_charges + 1) / 2
    # Calculate colors
    color_map = plt.get_cmap(CMAP_NAME)
    colors = color_map(normalized_charges)

    # Ball size should be proportional to VdW radius of the respective atom
    ball_sizes = np.array(
        [info.vdw_radius_single(e) for e in molecule.element]
    ) * BALL_SCALE

    # Gradient of ray strength
    # The ray size is proportional to the absolute charge value
    ray_full_sizes = ball_sizes + np.abs(charges) * RAY_SCALE
    ray_sizes = np.array([
        np.linspace(ray_full_sizes[i], ball_sizes[i], N_RAY_STEPS, endpoint=False)
        for i in range(molecule.array_length())
    ]).T


    # The plotting begins here
    fig = plt.figure(figsize=(8.0, 6.0))
    ax = fig.add_subplot(111, projection="3d")

    # Plot the atoms
    # As 'axes.scatter()' uses sizes in points**2,
    # the VdW-radii as also squared
    graphics.plot_ball_and_stick_model(
        ax, molecule, colors, ball_size=ball_sizes**2, line_width=3,
        line_color=color_map(0.5), background_color=(.05, .05, .05), zoom=1.5
    )

    # Plot the element labels
    for atom in molecule:
        ax.text(
            *atom.coord, atom.element,
            fontsize=ELEMENT_FONT_SIZE, color="black",
            ha="center", va="center", zorder=100
        )

    # Plot the rays
    for i in range(N_RAY_STEPS):
        ax.scatter(
            *molecule.coord.T, s=ray_sizes[i]**2, c=colors,
            linewidth=0, alpha=RAY_ALPHA
        )

    # Plot the colorbar
    color_bar = fig.colorbar(
        ScalarMappable(
            norm=Normalize(vmin=-max_charge, vmax=max_charge),
            cmap=color_map
        ),
        ax=ax
    )
    color_bar.set_label("Partial charge (e)", color="white")
    color_bar.ax.yaxis.set_tick_params(color="white")
    color_bar.outline.set_edgecolor("white")
    for label in color_bar.ax.get_yticklabels():
        label.set_color("white")

    fig.tight_layout()
    plt.show()

.. _sphx_glr_download_examples_gallery_structure_peoe_visualization.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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