aaindex – AAIndex annotations¶

class AAIndex(aaindex_files=None)¶

Provides access to data from the amino acid index database (aaindex):

Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000).

Files are available here

Parameters:

aaindex_files (list of str) – Paths to aaindex files. If not given, the files aaindex1, aaindex2 and aaindex3 from the specified source are used (Release 9.2, Feb 2017).

__getitem__(key)¶

Getter by aaindex accession number (e.g. ANDN920101)

Parameters:

key (str) – aaindex accession number

Returns:

AAIndexData object

keys()¶

Emulate dict like behvaiour and returns all available keys, accession numbers respectively.

Returns:

keys (or accession numbers) of all available aaindex entries

values()¶

Emulate dict like behvaiour and returns all available entries.

Returns:

iterable of entries (type AAIndexData)

The annotations/scores can either refer to single amino acids or represent pairwise values. The two types are:

class AnnoType(value)¶

Possible types of aaindex entries

PAIR = 'PAIR'¶

Pairwise amino acid annotation, substitution/pairwise scores

SINGLE = 'SINGLE'¶

Single amino acid annotation

The actual data of an entry in the aaindex database is stored in a aaindex.AAIndexData object:

class AAIndexData¶

Data object representing an annotation in aaindex, preferably constructed from it’s static 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 (AnnoType) specifying whether we’re dealing

  with a single or pairwise amino acid annotation/score.

• anno: 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 float (None if not available).

GetPairScore(olc_one, olc_two)¶

Score/Annotation getter

Parameters:

• olc_one (string) – One letter code of first amino acid

• olc_two (string) – One letter code of second amino acid

Returns:

Pairwise annotation/score for olc_one/olc_two

Raises:

ValueError if key constructed from olc_one and olc_two is not known or RuntimeError if anno_type of this AAIndexData object is not AnnoType.PAIR.

GetScore(olc)¶

Score/Annotation getter

Parameters:

olc (string) – One letter code of amino acid

Returns:

Annotation/score for olc

Raises:

ValueError if olc is not known or RuntimeError if anno_type of this AAIndexData object is not AnnoType.SINGLE.

static Parse(data)¶

Creates AAIndexData from data.

Parameters:

data – Iterable with strings in data format described for aaindex.

Returns:

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