Bio.PDB.HSExposure._AbstractHSExposure

Class _AbstractHSExposure

object --+ | AbstractPropertyMap.AbstractPropertyMap --+ | _AbstractHSExposure

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}

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.

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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__

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)

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.

Class _AbstractHSExposure

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

_get_gly_cb_vector(self, residue)

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