PyProteinAAIndex 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
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PyProteinAAIndex.
GetAAIndex1
(name, path='.')[source]¶ 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
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PyProteinAAIndex.
GetAAIndex23
(name, path='.')[source]¶ 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
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class
PyProteinAAIndex.
MatrixRecord
[source]¶ Bases:
PyProteinAAIndex.Record
Matrix record for mutation matrices or pair-wise contact potentials
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class
PyProteinAAIndex.
Record
[source]¶ Amino acid index (AAindex) Record
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aakeys
= 'ARNDCQEGHILKMFPSTWYV'¶
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PyProteinAAIndex.
grep
(pattern)[source]¶ Search for pattern in title and description of all records (case insensitive) and print results on standard output.
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PyProteinAAIndex.
init
(path=None, index='123')[source]¶ 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.