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#
# = bio/sequence/aa.rb - amino acid sequence class
#
# Copyright:: Copyright (C) 2006
# Toshiaki Katayama <k@bioruby.org>,
# Ryan Raaum <ryan@raaum.org>
# License:: The Ruby License
#
module Bio
autoload :AminoAcid, 'bio/data/aa' unless const_defined?(:AminoAcid)
require 'bio/sequence' unless const_defined?(:Sequence)
class Sequence
# = DESCRIPTION
# Bio::Sequence::AA represents a bare Amino Acid sequence in bioruby.
#
# = USAGE
# # Create an Amino Acid sequence.
# aa = Bio::Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
#
# # What are the three-letter codes for all the residues?
# puts aa.codes
#
# # What are the names of all the residues?
# puts aa.names
#
# # What is the molecular weight of this peptide?
# puts aa.molecular_weight
class AA < String
include Bio::Sequence::Common
# Generate an amino acid sequence object from a string.
#
# s = Bio::Sequence::AA.new("RRLEHTFVFLRNFSLMLLRY")
#
# or maybe (if you have an amino acid sequence in a file)
#
# s = Bio::Sequence:AA.new(File.open('aa.txt').read)
#
# Amino Acid sequences are *always* all uppercase in bioruby
#
# s = Bio::Sequence::AA.new("rrLeHtfV")
# puts s #=> "RRLEHTFVF"
#
# Whitespace is stripped from the sequence
#
# s = Bio::Sequence::AA.new("RRL\nELA\tRG\r RL")
# puts s #=> "RRLELARGRL"
# ---
# *Arguments*:
# * (required) _str_: String
# *Returns*:: Bio::Sequence::AA object
def initialize(str)
super
self.upcase!
self.tr!(" \t\n\r",'')
end
# Estimate molecular weight based on
# Fasman1976[http://www.genome.ad.jp/dbget-bin/www_bget?aaindex+FASG760101]
#
# s = Bio::Sequence::AA.new("RRLE")
# puts s.molecular_weight #=> 572.655
# ---
# *Returns*:: Float object
def molecular_weight
Bio::AminoAcid.weight(self)
end
# Create a ruby regular expression instance
# (Regexp)[http://corelib.rubyonrails.org/classes/Regexp.html]
#
# s = Bio::Sequence::AA.new("RRLE")
# puts s.to_re #=> /RRLE/
# ---
# *Returns*:: Regexp object
def to_re
Bio::AminoAcid.to_re(self)
end
# Generate the list of the names of each residue along with the
# sequence (3 letters code). Codes used in bioruby are found in the
# Bio::AminoAcid::NAMES hash.
#
# s = Bio::Sequence::AA.new("RRLE")
# puts s.codes #=> ["Arg", "Arg", "Leu", "Glu"]
# ---
# *Returns*:: Array object
def codes
array = []
self.each_byte do |x|
array.push(Bio::AminoAcid.names[x.chr])
end
return array
end
# Generate the list of the names of each residue along with the
# sequence (full name). Names used in bioruby are found in the
# Bio::AminoAcid::NAMES hash.
#
# s = Bio::Sequence::AA.new("RRLE")
# puts s.names
# #=> ["arginine", "arginine", "leucine", "glutamic acid"]
# ---
# *Returns*:: Array object
def names
self.codes.map do |x|
Bio::AminoAcid.names[x]
end
end
end # AA
end # Sequence
end # Bio
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