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 Loading Protein. After this, we will calculate a property and a shape to plot.

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

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.

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.

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]