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