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Package Bio :: Package PDB :: Module HSExposure :: Class _AbstractHSExposure
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Class _AbstractHSExposure

source code

                             object --+    
                                      |    
AbstractPropertyMap.AbstractPropertyMap --+
                                          |
                                         _AbstractHSExposure
Known Subclasses:

Abstract class to calculate Half-Sphere Exposure (HSE).

The HSE can be calculated based on the CA-CB vector, or the pseudo CB-CA vector based on three consecutive CA atoms. This is done by two separate subclasses.

Instance Methods [hide private]
 
__init__(self, model, radius, offset, hse_up_key, hse_down_key, angle_key=None)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
 
_get_cb(self, r1, r2, r3)
This method is provided by the subclasses to calculate HSE.		 source code
 
_get_gly_cb_vector(self, residue)
Return a pseudo CB vector for a Gly residue.		 source code

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

Inherited from AbstractPropertyMap.AbstractPropertyMap (private): _translate_id

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, model, radius, offset, hse_up_key, hse_down_key, angle_key=None)
(Constructor)

source code 

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
  • model (Model) - model
  • radius (float) - HSE radius
  • offset (int) - number of flanking residues that are ignored in the calculation of the number of neighbors
  • hse_up_key (string) - key used to store HSEup in the entity.xtra attribute
  • hse_down_key (string) - key used to store HSEdown in the entity.xtra attribute
  • angle_key (string) - key used to store the angle between CA-CB and CA-pCB in the entity.xtra attribute
Overrides: object.__init__

_get_gly_cb_vector(self, residue)

source code 

Return a pseudo CB vector for a Gly residue. The pseudoCB vector is centered at the origin.

CB coord=N coord rotated over -120 degrees along the CA-C axis.


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