AAIndexData Class Reference

Public Member Functions
def	__init__ (self)
def	GetScore (self, olc)
def	GetPairScore (self, olc_one, olc_two)

Static Public Member Functions
def	Parse (data)

Data Fields
	key
	desc
	ref
	authors
	title
	journal
	anno_type
	anno

Detailed Description

Data object representing an annotation in aaindex, preferably 
constructed from it's static :func:`Parse` method. The following 
attributes are available:

* key: aaindex accession number (e.g. ANDN920101)
* desc: descriptive title
* ref: Reference to article if available
* authors: Authors of article if available
* title: Title of article if available
* journal: Journal of article if available
* anno_type: Enum (:class:`AnnoType`) specifying whether we're dealing 
             with a single or pairwise amino acid annotation/score.
* anno: :class:`dict` with annotation. If *anno_type* is SINGLE,
        keys are amino acid one letter codes (single character strings).
        If *anno_type* is PAIR, keys are two one letter codes added 
        together (two character strings). Even when the thing is 
        symmetric, both keys exist. I.e. 'AB' AND 'BA'.
        Values are of type :class:`float` (None if not available).

Definition at line 21 of file aaindex.py.

Constructor & Destructor Documentation

__init__()

def __init__

(

self

)

Definition at line 41 of file aaindex.py.

Member Function Documentation

GetPairScore()

def GetPairScore	(		self,
			olc_one,
			olc_two
	)

Score/Annotation getter

:param olc_one: One letter code of first amino acid
:type olc_one: :class:`string`
:param olc_two: One letter code of second amino acid
:type olc_two: :class:`string`
:returns: Pairwise annotation/score for *olc_one*/*olc_two*
:raises: :class:`ValueError`  if key constructed from *olc_one* and 
         *olc_two* is not known or 
         :class:`RuntimeError` if anno_type of this 
         :class:`AAIndexData` object is not AnnoType.PAIR.

Definition at line 228 of file aaindex.py.

GetScore()

def GetScore	(		self,
			olc
	)

Score/Annotation getter

:param olc: One letter code of amino acid
:type olc: :class:`string`
:returns: Annotation/score for *olc*
:raises: :class:`ValueError` if *olc* is not known or 
         :class:`RuntimeError` if anno_type of this 
         :class:`AAIndexData` object is not AnnoType.SINGLE.

Definition at line 210 of file aaindex.py.

Parse()

def Parse (   data )

static

Creates :class:`AAIndexData` from data.

:param data: Iterable with strings in data format described for aaindex.
:returns: :class:`AAIndexData`, if iterable contains several entries, 
           parsing stops at separation sequence ('//'). None is returned
           if nothing could be parsed.
:raises: descriptive error in case of corrupt data

Definition at line 52 of file aaindex.py.

Field Documentation

anno

anno

Definition at line 49 of file aaindex.py.

anno_type

anno_type

Definition at line 48 of file aaindex.py.

authors

authors

Definition at line 45 of file aaindex.py.

desc

desc

Definition at line 43 of file aaindex.py.

journal

journal

Definition at line 47 of file aaindex.py.

key

key

Definition at line 42 of file aaindex.py.

ref

ref

Definition at line 44 of file aaindex.py.

title

title

Definition at line 46 of file aaindex.py.

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The documentation for this class was generated from the following file:

• build-dev-doc/stage/lib64/python3.9/site-packages/ost/seq/alg/aaindex.py