Bio.PDB.HSExposure module

Half-sphere exposure and coordination number calculation.

class Bio.PDB.HSExposure.HSExposureCA(model, radius=12, offset=0)

Bases: _AbstractHSExposure

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

Uses three consecutive CA positions.

__init__(model, radius=12, offset=0)

Initialize class.

Parameters:

  • model (L{Model}) – the model that contains the residues

  • radius (float) – radius of the sphere (centred at the CA atom)

  • offset (int) – number of flanking residues that are ignored in the calculation of the number of neighbors

pcb_vectors_pymol(filename='hs_exp.py')

Write PyMol script for visualization.

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

Parameters:

filename (string) – the name of the pymol script file

class Bio.PDB.HSExposure.HSExposureCB(model, radius=12, offset=0)

Bases: _AbstractHSExposure

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

__init__(model, radius=12, offset=0)

Initialize class.

Parameters:

  • model (L{Model}) – the model that contains the residues

  • radius (float) – radius of the sphere (centred at the CA atom)

  • offset (int) – number of flanking residues that are ignored in the calculation of the number of neighbors

class Bio.PDB.HSExposure.ExposureCN(model, radius=12.0, offset=0)

Bases: AbstractPropertyMap

Residue exposure as number of CA atoms around its CA atom.

__init__(model, radius=12.0, offset=0)

Initialize class.

A residue’s exposure is defined as the number of CA atoms around that residue’s CA atom. A dictionary is returned that uses a L{Residue} object as key, and the residue exposure as corresponding value.

Parameters:

  • model (L{Model}) – the model that contains the residues

  • radius (float) – radius of the sphere (centred at the CA atom)

  • offset (int) – number of flanking residues that are ignored in the calculation of the number of neighbors