Package csb :: Package bio :: Package sequence :: Module alignment :: Class AbstractScoringMatrix

Class AbstractScoringMatrix

object --+
         |
        AbstractScoringMatrix

Known Subclasses:

Defines a pairwise sequence alignment scoring function.

Nested Classes
	__metaclass__ Metaclass for defining Abstract Base Classes (ABCs).

Instance Methods

float

score(self, x, y)
Return the pairwise score of residues x and y. source code

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

Class Variables
	__abstractmethods__ = `frozenset(['score'])`

Properties
Inherited from `object`: `__class__`

Method Details

score(self, x, y)

source code

Return the pairwise score of residues x and y. x and y must be comparable (e.g. implement __eq__ and __hash__).

Parameters:

x (object) - first residue
y (object) - second residue

Returns: float

Raises:

ResidueNotFoundError - if x or y cannot be handled by this scoring matrix