AAIndex module

This module is used for obtaining the properties of amino acids or their pairs

from the aaindex database. You can freely use and distribute it. If you hava

any problem, you could contact with us timely!

Authors: Zhijiang Yao and Dongsheng Cao.

Date: 2016.06.04

Email: gadsby@163.com

AAIndex.GetAAIndex1(name, path='.')

Get the amino acid property values from aaindex1

Usage:

result=GetAAIndex1(name)

Input: name is the name of amino acid property (e.g., KRIW790103)

Output: result is a dict form containing the properties of 20 amino acids

AAIndex.GetAAIndex23(name, path='.')

Get the amino acid property values from aaindex2 and aaindex3

Usage:

result=GetAAIndex23(name)

Input: name is the name of amino acid property (e.g.,TANS760101,GRAR740104)

Output: result is a dict form containing the properties of 400 amino acid pairs

class AAIndex.MatrixRecord

Bases: AAIndex.Record

Matrix record for mutation matrices or pair-wise contact potentials

extend(row)

get(aai, aaj, d=None)

median()

class AAIndex.Record

Amino acid index (AAindex) Record

aakeys = 'ARNDCQEGHILKMFPSTWYV'

extend(row)

get(aai, aaj=None, d=None)

median()

AAIndex.get(key)

Get record for key

AAIndex.grep(pattern)

Search for pattern in title and description of all records (case insensitive) and print results on standard output.

AAIndex.init(path=None, index='123')

Read in the aaindex files. You need to run this (once) before you can access any records. If the files are not within the current directory, you need to specify the correct directory path. By default all three aaindex files are read in.

AAIndex.init_from_file(filename, type=<class AAIndex.Record at 0x03D525A8>)

AAIndex.search(pattern, searchtitle=True, casesensitive=False)

Search for pattern in description and title (optional) of all records and return matched records as list. By default search case insensitive.