9I3S Shape
==========

.. figure:: ../../_static/Gallery/9I3S_Shape_Size_plot.png
   :figclass: code-output
   :width: 100%
   :align: center


``9i3s.pdb`` File is required for the code below, you can obtain the 
protein structure from `RCSB Via Link <https://www.rcsb.org/structure/9I3S>`_

.. code-block:: python
    :caption: Code To Produce Above Plot

    import ProteoTwirl.ProteinRotation as pt
    from matplotlib.ticker import FuncFormatter
    import matplotlib.pyplot as plt
    import cartopy.crs as ccrs


    protein_structure = pt.ProteinRotation(
        protein                 = "9i3s.pdb",
        selection               = "protein and not element H",
        base_rotation           = "principle",
        center_selection        = True,
        atom_radii              = "vdw",
        default_rotation_res    = 32, 
        )


    protein_structure.add_property(
        property        = "Alphashape",
        alpha           = 0.25,
        hole_fill       = 0.01,
        workers         = 1

    )
    protein_structure.add_property(
        property="shape.area",
    )

    fig, ax = protein_structure.plot_shape(
        shape_size          =50, 
        figsize             =(10,6),
        color_property      ="Alpha_Shape_25_HF1_area", 
        shape_color         ="#222244aa",
        contour_color       ="plasma", 
        gridlines           = {
                                "linewidth"     :1, 
                                "colors"        :"#ffffff", 
                                "edgecolor"     :"#999999",
                                "dms"           :True
                            },
        contour_lines       = {
                                "linewidths"    : 0.5,
                                "colors"        :"#dddddd" 
                            },
        contour_labels      = {
                                "colors"        : "#ffffff", 
                                "fmt"           : FuncFormatter(lambda value, pos: r"{:.0f} $\cdot 10^3$".format(value / 1000))
                            },
        projection          = ccrs.EckertII(),
        )

    plt.tight_layout()

    fig.patch.set_alpha(0)
    ax.patch.set_alpha(0)