.. _gallery7gdc :

6GDC Hydropahy
==============



.. raw:: html

   <figure class="code-output iframe-output">
   <iframe
     src="../_static/Gallery/6GDC_Gallery.html"
     style="width:100%; height:750px; border:none;"
     loading="lazy"
   ></iframe>
   </figure>

This 3D visualization show the selection of atoms together with the hydropathy 
index of each residue, and the average hydropathy index of each angle. This 
system and calculation is covered in more detail in the :ref:`bindingpocket`
tutorial.


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


    import ProteoTwirl.ProteinRotation as pt
    import MDAnalysis as mda
    import numpy as np
    from ProteoTwirl.Visualization.Plot3D import plot_property_3d, plot_3d,_value_color_func, _value_size_func
    from ProteoTwirl.Selectors.Selector import ExposedAtomSelector, ClippingPlaneSelector, FieldOfViewSelector

    #╭────────────────────────────────────────────────────────╮#
    #│               LOAD & CALCULATE HYDROPATHY              │#
    #╰────────────────────────────────────────────────────────╯#

    # Get Ligand Center - For Binding Pocket Position
    universe    = mda.Universe("Test_Data/6GDC.pdb")
    ligand      = universe.select_atoms("resname FB2 and resid 305")
    ligand_cog  = np.mean(ligand.positions, axis = 0)


    # Load Protein Centered on Binding Pocket
    protein_structure = pt.ProteinRotation(
        protein                 = "Test_Data/6GDC.pdb",
        selection               = "protein and not element H",
        base_rotation           = None,
        center_selection        = False,
        center                  = ligand_cog,
        )


    # Calculate Hydropathy for Binding Pocket
    protein_structure.add_property(
        property            ="count.Hydropathy",
        rotation_res        =  128,
        agg_method          = "mean",
        use_default         =False,
        rotation_range      =  None,
        selectors           = [
                                ClippingPlaneSelector((None,0)),
                                FieldOfViewSelector(7),
                                ExposedAtomSelector()
                            ]
    )


    #╭────────────────────────────────────────────────────────╮#
    #│                        SET COLOR                       │#
    #╰────────────────────────────────────────────────────────╯#

    # Set color per angle 
    min_val     = np.min(protein_structure.mean_Hydropathy)
    max_val     = np.max(protein_structure.mean_Hydropathy)


    def color_white_selection (index, angle, val, cur_angle): 

        if cur_angle : 
            return "#ffffff"

        return _value_color_func(index, angle, val, cur_angle,min_val,max_val-min_val, "plasma")

    color_val   = lambda index, angle, val, cur_angle : color_white_selection (index, angle, val, cur_angle)


    #╭────────────────────────────────────────────────────────╮#
    #│                       SET RADIUS                       │#
    #╰────────────────────────────────────────────────────────╯#

    def size_selection (index, angle, val, cur_angle): 

        if cur_angle : 
            return 12.5

        return _value_size_func(index, angle, val, cur_angle,min_val,max_val-min_val, (1,10))

    size_val   = lambda index, angle, val, cur_angle : size_selection (index, angle, val, cur_angle)



    #╭────────────────────────────────────────────────────────╮#
    #│                  GET SELECTED INDICES                  │#
    #╰────────────────────────────────────────────────────────╯#

    # Get Atom Selections for Binding Pocket
    prot_it = protein_structure.iter(
        rotation_res    =  128,
        selectors       = [
                            ClippingPlaneSelector((None,0)),
                            FieldOfViewSelector(7),
                            ExposedAtomSelector()
                        ]
    )


    md_atom_selection = []
    selections        = []
    for it_positions,it_atom,it_indices in prot_it : 
        md_atom_selection.append(it_atom)
        selections.append(it_indices) 

    plot_3d(
        protein_rotation    = protein_structure,
        selections          = selections,
        angles              = protein_structure._angle_spaces[0],
        values              = protein_structure.mean_Hydropathy,
        selected_color      = "Hydropathy Index",
        selected_radius     = 1.5,
        unselected_radius   = 0.25,
        unselected_color    = "Hydropathy Index",
        angle_color         = color_val,
        angle_radius        = size_selection,
        background          = "#14181e",
        html_path           = "6GDC_Gallery.html"

    )