Package csb :: Package bio :: Package sequence :: Module alignment :: Class SimilarityMatrix |
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# Class SimilarityMatrix

source code

               object --+
                        |
    AbstractScoringMatrix --+
                            |
                           SimilarityMatrix

Similarity scoring matrix.

Nested Classes
Inherited from `AbstractScoringMatrix`: `__metaclass__`

Instance Methods
__init__(self, matrix=`{``'``*``'``:` `{``'``*``'``:` 1.0`,` `'``A``'``:` -4.0`,` `'``B``'``:` -4.0`,` `'``C``'``:` -4.0`,` `'``D``'``:` -4.0`,` `'``...`) x.__init__(...) initializes x; see help(type(x)) for signature | source code
float |
score(self, x, y) Return the pairwise score of residues `x` and `y`. | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Static Methods
SimilarityMatrix |
parse(string) Parse a standard scoring matrix file, where the first row and column are residue labels. | source code

Class Variables
| BLOSUM62 = ``{``'``*``'``:` `{``'``*``'``:` 1.0`,` `'``A``'``:` -4.0`,` `'``B``'``:` -4.0`,` `'``C``'``:` -4.0`,` `'``...``
| __abstractmethods__ = ``frozenset([``])``

Properties
Inherited from `object`: `__class__`

Method Details

### __init__(self, matrix=`{``'``*``'``:` `{``'``*``'``:` 1.0`,` `'``A``'``:` -4.0`,` `'``B``'``:` -4.0`,` `'``C``'``:` -4.0`,` `'``D``'``:` -4.0`,` `'``...`) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `matrix` Overrides: object.__init__ (inherited documentation)

### parse(string) Static Method | source code
Parse a standard scoring matrix file, where the first row and column are residue labels. Parameters: `string` (str) - scoring matrix string Returns: SimilarityMatrix

### 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` - first residue `y` - second residue Returns: float Raises: `ResidueNotFoundError` - if `x` or `y` cannot be handled by this scoring matrix Overrides: AbstractScoringMatrix.score (inherited documentation)

Class Variable Details

  ### BLOSUM62 Value:
      {'*': {'*': 1.0,
             'A': -4.0,
             'B': -4.0,
             'C': -4.0,
             'D': -4.0,
             'E': -4.0,
             'F': -4.0,
             'G': -4.0,
      ...