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