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

Class HSExposureCA

                             object --+        
                                      |        
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)
@param model: the model that contains the residues @type model: L{Model}

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: __contains__, __getitem__, __iter__, __len__, has_key, keys

Inherited from AbstractPropertyMap.AbstractPropertyMap (private): _translate_id

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

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

source code


@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)

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.

@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

Class HSExposureCA

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

_get_cb(self, r1, r2, r3)

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

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

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