Package Bio :: Package PDB :: Module HSExposure :: Class HSExposureCA
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Class HSExposureCA

source code

AbstractPropertyMap.AbstractPropertyMap --+    
                                          |    
                        _AbstractHSExposure --+
                                              |
                                             HSExposureCA

Class to calculate HSE based on the approximate CA-CB vectors, using three consecutive CA positions.

Instance Methods [hide private]
 
__init__(self, model, radius=12, offset=0) source code
 
_get_cb(self, r1, r2, r3)
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.
source code
 
pcb_vectors_pymol(self, filename='hs_exp.py')
Write a PyMol script that visualizes the pseudo CB-CA directions at the CA coordinates.
source code

Inherited from _AbstractHSExposure (private): _get_gly_cb_vector

Inherited from AbstractPropertyMap.AbstractPropertyMap: __getitem__, __iter__, __len__, has_key, keys

Method Details [hide private]

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

source code 
Parameters:
  • model (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
Overrides: AbstractPropertyMap.AbstractPropertyMap.__init__

_get_cb(self, r1, r2, r3)

source code 

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.

Parameters:
  • r1, r2, r3 - three consecutive residues

pcb_vectors_pymol(self, filename='hs_exp.py')

source code 

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