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

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                             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)
@param model: model @type model: L{Model}
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_get_cb(self, r1, r2, r3)
This method is provided by the subclasses to calculate HSE.
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_get_gly_cb_vector(self, residue)
Return a pseudo CB vector for a Gly residue.
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Inherited from AbstractPropertyMap.AbstractPropertyMap: __contains__, __getitem__, __iter__, __len__, has_key, keys

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)

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@param model: model
@type model: L{Model}

@param radius: HSE radius
@type radius: float

@param offset: number of flanking residues that are ignored in the calculation
of the number of neighbors
@type offset: int

@param hse_up_key: key used to store HSEup in the entity.xtra attribute
@type hse_up_key: string

@param hse_down_key: key used to store HSEdown in the entity.xtra attribute
@type hse_down_key: string

@param angle_key: key used to store the angle between CA-CB and CA-pCB in
    the entity.xtra attribute
@type angle_key: string

Overrides: object.__init__

_get_gly_cb_vector(self, residue)

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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.