class Bio::Sequence::AA

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

Public Class Methods

new (str)

Source

   # File lib/bio/sequence/aa.rb
58 def initialize(str)
59   super
60   self.upcase!
61   self.tr!(" \t\n\r",'')
62 end

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

Calls superclass method

randomize (*arg, &block)

Source

    # File lib/bio/sequence/compat.rb
113 def self.randomize(*arg, &block)
114   self.new('').randomize(*arg, &block)
115 end

Generate a new random sequence with the given frequency of bases. The sequence length is determined by their cumulative sum. (See also Bio::Sequence::Common#randomize which creates a new randomized sequence object using the base composition of an existing sequence instance).

counts = {'R'=>1,'L'=>2,'E'=>3,'A'=>4}
puts Bio::Sequence::AA.randomize(counts)  #=> "AAEAELALRE" (for example)

You may also feed the output of randomize into a block

actual_counts = {'R'=>0,'L'=>0,'E'=>0,'A'=>0}
Bio::Sequence::AA.randomize(counts) {|x| actual_counts[x] += 1}
actual_counts                     #=> {"A"=>4, "L"=>2, "E"=>3, "R"=>1}

Arguments:

(optional) hash: Hash object

Returns: Bio::Sequence::AA object

Public Instance Methods

codes ()

Source

    # File lib/bio/sequence/aa.rb
 95 def codes
 96   array = []
 97   self.each_byte do |x|
 98     array.push(Bio::AminoAcid.names[x.chr])
 99   end
100   return array
101 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

molecular_weight ()

Source

   # File lib/bio/sequence/aa.rb
72 def molecular_weight
73   Bio::AminoAcid.weight(self)
74 end

Estimate molecular weight based on Fasman1976

s = Bio::Sequence::AA.new("RRLE")
puts s.molecular_weight             #=> 572.655

Returns: Float object

names ()

Source

    # File lib/bio/sequence/aa.rb
112 def names
113   self.codes.map do |x|
114     Bio::AminoAcid.names[x]
115   end
116 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

to_re ()

Source

   # File lib/bio/sequence/aa.rb
83 def to_re
84   Bio::AminoAcid.to_re(self)
85 end

Create a ruby regular expression instance (Regexp)

s = Bio::Sequence::AA.new("RRLE")
puts s.to_re                        #=> /RRLE/

Returns: Regexp object