Package csb :: Package bio :: Package fragments :: Module isites :: Class ProteinProfile

Class ProteinProfile

object --+
         |
        ProteinProfile

Describes an I-Sites protein profile/PSSM.

Instance Methods

__init__(self, background={'A': 0.07705, 'B': 0.051935, 'C': 0.01614, 'D': 0.05847, 'E':..., matrix=None, alpha=0.2)
x.__init__(...) initializes x; see help(type(x)) for signature source code

int

add_column(self, **target_frequencies)
Append a new column to the profile.

source code

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

Class Variables
	BackgroundFreqs = `{'A': 0.07705, 'B': 0.051935, 'C': 0.01614, ...`

Properties
	length
	matrix
	max_score
	pssm
Inherited from `object`: `__class__`

Method Details

init(self, background=`{'A':` 0.07705`,` `'B':` 0.051935`,` `'C':` 0.01614`,` `'D':` 0.05847`,` `'E':...`, matrix=None, alpha=0.2)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

background (dict) - background amino acid frequencies
matrix (dict) - initialization array with target frequencies
alpha (float) - fixed "pseudocount" number for this cluster/profile

Overrides: object.__init__

(inherited documentation)

add_column(self, **target_frequencies)

source code

Append a new column to the profile.

Keyword arguments are used to pass the individual amino acid target frequencies, e.g. A=0.12, B=0.0, etc. If an amino acid is omitted, its probability will be set automatically to 0.

Parameters:

target_frequencies (dict) - amino acid frequencies in that column

Returns: int

the index of the new column

Raises:

KeyError - if the target frequencies dict contains an unknown amino acid with respect to profile.background

Class Variable Details

BackgroundFreqs

Value:

{'A': 0.07705,
 'B': 0.051935,
 'C': 0.01614,
 'D': 0.05847,
 'E': 0.06564,
 'F': 0.04109,
 'G': 0.07218,
 'H': 0.02363,
...

Property Details

length

Get Method:: unreachable.length(self)

matrix

Get Method:: unreachable.matrix(self)

max_score

Get Method:: unreachable.max_score(self)

pssm

Get Method:: unreachable.pssm(self)

Class ProteinProfile

__init__(self, background={'A': 0.07705, 'B': 0.051935, 'C': 0.01614, 'D': 0.05847, 'E':..., matrix=None, alpha=0.2) (Constructor)

add_column(self, **target_frequencies)

BackgroundFreqs

length

matrix

max_score

pssm

init(self, background=`{'A':` 0.07705`,` `'B':` 0.051935`,` `'C':` 0.01614`,` `'D':` 0.05847`,` `'E':...`, matrix=None, alpha=0.2)
(Constructor)