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

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                             object --+        
                                      |        
AbstractPropertyMap.AbstractPropertyMap --+    
                                          |    
                        _AbstractHSExposure --+
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                                             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)
@param model: the model that contains the residues @type model: L{Model}
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_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.
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pcb_vectors_pymol(self, filename='hs_exp.py')
Write a PyMol script that visualizes the pseudo CB-CA directions at the CA coordinates.
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Inherited from _AbstractHSExposure (private): _get_gly_cb_vector

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=12, offset=0)
(Constructor)

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@param model: the model that contains the residues @type model: L{Model}

@param radius: radius of the sphere (centred at the CA atom) @type radius: float

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

Overrides: object.__init__

_get_cb(self, r1, r2, r3)

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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.

@param r1, r2, r3: three consecutive residues @type r1, r2, r3: L{Residue}

Overrides: _AbstractHSExposure._get_cb

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.

@param filename: the name of the pymol script file @type filename: string