biopython v1.71.0 Bio.PDB.HSExposure.HSExposureCA

Class to calculate HSE based on the approximate CA-CB vectors.

Uses three consecutive CA positions.

Link to this section Summary


Initialse class

Calculate approx CA-CB direction (PRIVATE)

Write PyMol script for visualization

Link to this section Functions

Initialse class.

:param model: the model that contains the residues :type model: L{Model}

:param radius: radius of the sphere (centred at the CA atom) :type radius: float

:param offset: number of flanking residues that are ignored

           in the calculation of the number of neighbors

:type offset: int

Calculate approx CA-CB direction (PRIVATE).

Calculate the approximate CA-CB direction for a central CA atom based on the two flanking CA positions, and the angle with the real CA-CB vector.

The CA-CB vector is centered at the origin.

:param r1, r2, r3: three consecutive residues :type r1, r2, r3: L{Residue}

Link to this function pcb_vectors_pymol()

Write PyMol script for visualization.

Write a PyMol script that visualizes the pseudo CB-CA directions at the CA coordinates.

:param filename: the name of the pymol script file :type filename: string