Class: MS::Peptide

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/sim_peptide.rb

Instance Method Summary collapse

Constructor Details

#initialize(sequence, charge, abu = 1.0, db, id, prot_id, modifications) ⇒ Peptide

Returns a new instance of Peptide.



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# File 'lib/ms/sim_peptide.rb', line 5

def initialize(sequence, charge, abu = 1.0,db,id,prot_id,modifications)
  @abu = abu
  @p_rt = 0
  @p_int = 0
  @rts = []
  @charge = charge 
  
  @mods = modifications

  spec = calcSpectrum(sequence)

  # TODO Ryan: alter this to handle variable and static mass modifications...Add it from the Katamari code

  #core mzs, ints
  db.execute "INSERT INTO core_spec VALUES(#{id},'#{spec.mzs}','#{spec.intensities}')"

  @mono_mz = spec.mzs[spec.intensities.index(spec.intensities.max)]
  @mass = @mono_mz * @charge
  #U,O,X ???
  @aa_counts = []
  stm = "INSERT INTO aac VALUES(#{id},"
  amino_acids = ['A','R','N','D','B','C','E','Q','Z','G','H','I',
    'L','K','M','F','P','S','T','W','Y','V','J']
  amino_acids.map do |aa|
    count = sequence.count(aa)
    stm<<"#{count},"
    count
  end
  stm<<"0.0)" #place holder for predicted values
  stm = db.prepare(stm)
  stm.execute
  stm.close if stm
  db.execute "INSERT INTO peptides VALUES(#{id},'#{sequence}', #{@mass}, #{charge}, #{@mono_mz}, #{@p_rt},NULL, #{@p_int}, #{@abu}, NULL,NULL,NULL,#{prot_id})"
end

Instance Method Details

#calcSpectrum(seq) ⇒ Object

Calculates theoretical specturm



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# File 'lib/ms/sim_peptide.rb', line 42

def calcSpectrum(seq)
  #isotope.rb from Dr. Prince
  atoms = countAtoms(seq)

  var = ""
  var<<"O"
  var<<atoms[0].to_s
  var<<"N"
  var<<atoms[1].to_s
  var<<"C"
  var<<atoms[2].to_s
  var<<"H"
  var<<atoms[3].to_s
  var<<"S"
  var<<atoms[4].to_s
  var<<"P"
  var<<atoms[5].to_s
  var<<"Se"
  var<<atoms[6].to_s

  mf = Mspire::MolecularFormula.from_string(var, @charge)
  spec = Mspire::Isotope::Distribution.spectrum(mf, :max, 0.001)

  spec.intensities.map!{|i| i = i*100.0}

  return spec
end

#countAtoms(seq) ⇒ Object

Counts the number of each atom in the peptide sequence.



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# File 'lib/ms/sim_peptide.rb', line 73

def countAtoms(seq)
  atom_indexes = {'O' => 0,'N' => 1,'C' => 2,'H' => 3,'S' => 4,'P' => 5,'Se' => 6}
  o = 0
  n = 0
  c = 0
  h = 0
  s = 0
  p = 0
  se = 0
  @charge.times {h += 1}
  atom_counts = [(o + 1),n,c,(h + 2),s,p,se]
  
  seq.each_char do |aa|
    #poly amino acids
    #maybe in the future ignore fringe case amino acids
    #"X" is for any (I exclude uncommon "U" and "O")
    if aa == "X"
      aas = Mspire::Isotope::AA::ATOM_COUNTS.keys[0..19]
      aa = aas[rand(20)]
      #"B" is "N" or "D"
    elsif aa == "B"
      aas = ["N","D"]
      aa = aas[rand(2)]
      #"Z" is "Q" or "E"
    elsif aa == "Z"
      aas = ["Q","E"]
      aa = aas[rand(2)]
    end
    
    #perform modification for residue
    if @mods != nil
      if @mods[aa] != nil
        mods = @mods[aa]
        mods.each do |mod|
          mod[1].split(/\s/).each_slice(2) do |sl|
            atom_counts[atom_indexes[sl[0]]] = atom_counts[atom_indexes[sl[0]]] + sl[1].to_i 
          end
        end
      elsif seq[0] == aa and @mods["CT"] != nil#N-terminus
        mods = @mods["CT"]
        mods.each do |mod|
          mod[1].split(/\s/).each_slice(2) do |sl|
            atom_counts[atom_indexes[sl[0]]] = atom_counts[atom_indexes[sl[0]]] + sl[1].to_i 
          end
        end
      elsif seq[-1] == aa and @mods["NT"] != nil#C-terminus
        mods = @mods["NT"]
        mods.each do |mod|
          mod[1].split(/\s/).each_slice(2) do |sl|
            atom_counts[atom_indexes[sl[0]]] = atom_counts[atom_indexes[sl[0]]] + sl[1].to_i 
          end
        end
      end
    end

    if aa !~ /A|R|N|D|C|E|Q|G|H|I|L|K|M|F|P|S|T|W|Y|V|U|O/
      puts "No amino acid match for #{aa}"
    else
      atom_counts[0] = atom_counts[0] + Mspire::Isotope::AA::ATOM_COUNTS[aa][:o]
      atom_counts[1] = atom_counts[1] + Mspire::Isotope::AA::ATOM_COUNTS[aa][:n]
      atom_counts[2] = atom_counts[2] + Mspire::Isotope::AA::ATOM_COUNTS[aa][:c]
      atom_counts[3] = atom_counts[3] + Mspire::Isotope::AA::ATOM_COUNTS[aa][:h]
      atom_counts[4] = atom_counts[4] + Mspire::Isotope::AA::ATOM_COUNTS[aa][:s]
      atom_counts[5] = atom_counts[5] + Mspire::Isotope::AA::ATOM_COUNTS[aa][:p]
      atom_counts[6] = atom_counts[6] + Mspire::Isotope::AA::ATOM_COUNTS[aa][:se]
    end
  end
  return atom_counts
end