Method: Bio::PDB::Chain#aaseq

Defined in:
lib/bio/db/pdb/chain.rb

#aaseq ⇒ Object Also known as: atom_seq

gets an amino acid sequence of this chain from ATOM records



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# File 'lib/bio/db/pdb/chain.rb', line 182

def aaseq
  unless defined? @aaseq
    string = ""
    last_residue_num = nil
    @residues.each do |residue|
      if last_residue_num and 
          (x = (residue.resSeq.to_i - last_residue_num).abs) > 1 then
        x.times { string << 'X' }
      end
      tlc = residue.resName.capitalize
      olc = (begin
               Bio::AminoAcid.three2one(tlc)
             rescue ArgumentError
               nil
             end || 'X')
      string << olc
    end
    @aaseq = Bio::Sequence::AA.new(string)
  end
  @aaseq
end