Module Bio::AminoAcid::Data
In: lib/bio/data/aa.rb  (CVS)

Methods

[]   aa   name   name2one   name2three   names   one   one2name   one2three   three   three2name   three2one   to_1   to_3   to_re   weight  

Constants

NAMES = { 'A' => 'Ala', 'C' => 'Cys', 'D' => 'Asp', 'E' => 'Glu', 'F' => 'Phe', 'G' => 'Gly', 'H' => 'His', 'I' => 'Ile', 'K' => 'Lys', 'L' => 'Leu', 'M' => 'Met', 'N' => 'Asn', 'P' => 'Pro', 'Q' => 'Gln', 'R' => 'Arg', 'S' => 'Ser', 'T' => 'Thr', 'V' => 'Val', 'W' => 'Trp', 'Y' => 'Tyr', 'B' => 'Asx', # D/N 'Z' => 'Glx', # E/Q 'J' => 'Xle', # I/L 'U' => 'Sec', # 'uga' (stop) 'O' => 'Pyl', # 'uag' (stop) 'X' => 'Xaa', # (unknown) 'Ala' => 'alanine', 'Cys' => 'cysteine', 'Asp' => 'aspartic acid', 'Glu' => 'glutamic acid', 'Phe' => 'phenylalanine', 'Gly' => 'glycine', 'His' => 'histidine', 'Ile' => 'isoleucine', 'Lys' => 'lysine', 'Leu' => 'leucine', 'Met' => 'methionine', 'Asn' => 'asparagine', 'Pro' => 'proline', 'Gln' => 'glutamine', 'Arg' => 'arginine', 'Ser' => 'serine', 'Thr' => 'threonine', 'Val' => 'valine', 'Trp' => 'tryptophan', 'Tyr' => 'tyrosine', 'Asx' => 'asparagine/aspartic acid [DN]', 'Glx' => 'glutamine/glutamic acid [EQ]', 'Xle' => 'isoleucine/leucine [IL]', 'Sec' => 'selenocysteine', 'Pyl' => 'pyrrolysine', 'Xaa' => 'unknown [A-Z]', }   IUPAC code
WEIGHT = { 'A' => 89.09, 'C' => 121.15, # 121.16 according to the Wikipedia 'D' => 133.10, 'E' => 147.13, 'F' => 165.19, 'G' => 75.07, 'H' => 155.16, 'I' => 131.17, 'K' => 146.19, 'L' => 131.17, 'M' => 149.21, 'N' => 132.12, 'P' => 115.13, 'Q' => 146.15, 'R' => 174.20, 'S' => 105.09, 'T' => 119.12, 'U' => 168.06, 'V' => 117.15, 'W' => 204.23, 'Y' => 181.19, }   AAindex FASG760101 - Molecular weight (Fasman, 1976) 
  Fasman, G.D., ed.
  Handbook of Biochemistry and Molecular Biology", 3rd ed.,
  Proteins - Volume 1, CRC Press, Cleveland (1976)

Public Instance methods

[](x)

[Source]

# File lib/bio/data/aa.rb, line 131
    def [](x)
      NAMES[x]
    end
aa()

Alias for names

name(x)

[Source]

# File lib/bio/data/aa.rb, line 141
    def name(x)
      str = NAMES[x]
      if str and str.length == 3
        NAMES[str]
      else
        str
      end
    end
name2one(x)

[Source]

# File lib/bio/data/aa.rb, line 198
    def name2one(x)
      str = reverse[x.to_s.downcase]
      if str and str.length == 3
        three2one(str)
      else
        str
      end
    end
name2three(x)

[Source]

# File lib/bio/data/aa.rb, line 215
    def name2three(x)
      reverse[x.downcase]
    end
names()

backward compatibility

[Source]

# File lib/bio/data/aa.rb, line 136
    def names
      NAMES
    end
one(x)

Alias for to_1

one2name(x)

[Source]

# File lib/bio/data/aa.rb, line 190
    def one2name(x)
      if x and x.length != 1
        raise ArgumentError
      else
        three2name(NAMES[x])
      end
    end
one2three(x)

[Source]

# File lib/bio/data/aa.rb, line 174
    def one2three(x)
      if x and x.length != 1
        raise ArgumentError
      else
        NAMES[x]
      end
    end
three(x)

Alias for to_3

three2name(x)

[Source]

# File lib/bio/data/aa.rb, line 207
    def three2name(x)
      if x and x.length != 3
        raise ArgumentError
      else
        NAMES[x]
      end
    end
three2one(x)

[Source]

# File lib/bio/data/aa.rb, line 182
    def three2one(x)
      if x and x.length != 3
        raise ArgumentError
      else
        reverse[x]
      end
    end
to_1(x)

[Source]

# File lib/bio/data/aa.rb, line 150
    def to_1(x)
      case x.to_s.length
      when 1
        x
      when 3
        three2one(x)
      else
        name2one(x)
      end
    end
to_3(x)

[Source]

# File lib/bio/data/aa.rb, line 162
    def to_3(x)
      case x.to_s.length
      when 1
        one2three(x)
      when 3
        x
      else
        name2three(x)
      end
    end
to_re(seq)

[Source]

# File lib/bio/data/aa.rb, line 219
    def to_re(seq)
      replace = {
        'B' => '[DNB]',
        'Z' => '[EQZ]',
        'J' => '[ILJ]',
        'X' => '[ACDEFGHIKLMNPQRSTVWYUOX]',
      }
      replace.default = '.'

      str = seq.to_s.upcase
      str.gsub!(/[^ACDEFGHIKLMNPQRSTVWYUO]/) { |aa|
        replace[aa]
      }
      Regexp.new(str)
    end
weight(x = nil)

[Source]

# File lib/bio/data/aa.rb, line 110
    def weight(x = nil)
      if x
        if x.length > 1
          total = 0.0
          x.each_byte do |byte|
            aa = byte.chr.upcase
            if WEIGHT[aa]
              total += WEIGHT[aa]
            else
              raise "Error: invalid amino acid '#{aa}'"
            end
          end
          total -= NucleicAcid.weight[:water] * (x.length - 1)
        else
          WEIGHT[x]
        end
      else
        WEIGHT
      end
    end

[Validate]