# aaindex.rb

Path: | lib/bio/db/aaindex.rb
Last Update: | Thu Nov 19 15:47:02 +0000 2009

# bio/db/aaindex.rb - AAindex database class

Copyright: | Copyright (C) 2001 KAWASHIMA Shuichi <s@bioruby.org>
Copyright: | Copyright (C) 2006 Mitsuteru C. Nakao <n@bioruby.org>
License: | The Ruby License

$Id: aaindex.rb,v 1.20 2007/04/05 23:35:40 trevor Exp $

## Description

Classes for Amino Acid Index Database (AAindex and AAindex2).

- AAindex Manual: www.genome.jp/dbget-bin/show_man?aaindex

## Examples

     aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")
     aax2 = Bio::AAindex.auto("DAYM780301.aaindex2")

     aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
     aax1.entry_id
     aax1.index

     aax2 = Bio::AAindex2.new("DAYM780301.aaindex2")
     aax2.entry_id
     aax2.matrix
     aax2.matrix[2,2]
     aax2.matrix('R', 'A')
     aax2['R', 'A']

## References

- www.genome.jp/aaindex/

### Required files

bio/db matrix bio/io/fetch

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