.. _vizexamplesys:

Visualization Example System
============================
All examples below will be created using the example system presented
below. In this setup, we will load ``8JXW`` with added hydrogens, as
done in :ref:`loading_protein`. After this, we will calculate a
property and a shape to plot.

.. code-block:: python
    :caption: Loading a Protein from PDB

    import ProteoTwirl.ProteinRotation as pt

    protein_structure = pt.ProteinRotation(
        protein                 = "8JXW_H.pdb",             # Protein structure to load
        selection               = "protein and segid E and not element H",  # Select receptor only (in this case segment E)
        base_rotation           = "principle",              # Align to principal axes
        center_selection        = True,                     # Set center of geometry to (0,0,0) (center of rotation)
        atom_radii              = "vdw",                    # Definition of radii to use, here van der Waals
        
        # Default values avoid having to re-enter them for each added property 
        default_rotation_res    = 128,                       # Number of angles to sample 
        default_rotation_range  = None,                     # Can be set to min and max values for theta and phi angles
        default_selectors       = None,                     # Allows us to select atoms based on orientation
        default_sampler         = None,                     # How we sample angles, currently only Fibonacci sphere
        )

    # Show interactive view of the protein loaded
    protein_structure


.. raw:: html

   <figure class="code-output iframe-output">
   <iframe
     src="../../_static/Guides/Loading/8JXW_Loaded.html"
     style="width:100%; height:300px; border:none;"
     loading="lazy"
   ></iframe>
   </figure>


Once the protein is loaded, we will calculate a property. In this case, we 
will calculate the average hydropathy index of the exposed residues of 
the protein. 

Hydropathy is a count property, and we can add it using the 
name ``"count.Hydropathy"``. We also need to set the aggregation method to 
``"mean"``; otherwise, no aggregation is performed, and we need one value
per angle to plot. 


.. code-block:: python
    :caption: Calculating Hydropathy of Exposed Residues

    from ProteoTwirl.Selectors.Selector import ExposedAtomSelector

    protein_structure.add_property(
        property        = "count.Hydropathy",
        agg_method      = "mean",

        use_default     = False,
        rotation_res    = 64,
        selectors       = [ExposedAtomSelector()],
        workers         = 1

    )

    >>> Adding mean_Hydropathy

    print(len(protein_structure.mean_Hydropathy))

    >>> 64

Lastly, we will construct a shape of the protein. Here, we will use an 
alpha shape and apply a small amount of hole filling to clean up the shape.

.. code-block:: python
    :caption: Calculating Alpha Shape of Protein

    protein_structure.add_property(
        property        = "Alphashape",
        hole_fill       = 0.2,

        use_default     = False,
        rotation_res    = 64,
        workers         = 1

    )

    >>> Adding Alpha_Shape_45_HF20

    print(len(protein_structure.Alpha_Shape_45_HF20))

    >>> 64

    protein_structure.Alpha_Shape_45_HF20[0]


.. figure:: ../../_static/Guides/Visualization/8JWX_H_AlphaShape_HF20.svg
   :figclass: code-output
   :width: 25%
   :align: center