Class: MS::ChargeCalculator

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

Defined Under Namespace

Classes: PepCharges

Constant Summary collapse

PkTable =

Returns the PepCharges structure

{
  :K => [2.18,8.95,10.53], 
  :E => [2.19,9.67,4.25], 
  :D => [1.88,9.60,3.65], 
  :H => [1.82,9.17,6.00],
  :R => [2.17,9.04,12.48],
  :Q => [2.17,9.13,nil],
  :N => [2.02,8.80,nil],
  :C => [1.96,10.28,8.18],
  :T => [2.11,9.62,nil],
  :S => [2.21,9.15,nil],
  :W => [2.38,9.39,nil],
  :Y => [2.20,9.11,10.07],
  :F => [1.83,9.13,nil],
  :M => [2.28,9.21,nil],
  :I => [2.36,9.68,nil],
  :L => [2.36,9.60,nil],
  :V => [2.32,9.62,nil],
  :P => [1.99,10.96,nil],
  :A => [2.34,9.69,nil],
  :G => [2.34,9.60,nil],
# These are the fringe cases... B and Z... Jerks, these are harder to calculate pIs
  :B => [1.95,9.20,3.65],
  :Z => [2.18,9.40,4.25],
  :X => [2.20,9.40,nil],
  :U => [1.96,10.28,5.20] # Unfortunately, I've only found the pKr for this... so I've used Cysteine's values.
}

Class Method Summary collapse

Class Method Details

.charge_at_pH(pep_charges, pH) ⇒ Object 



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# File 'lib/charge_calculator.rb', line 65

def self.charge_at_pH(pep_charges, pH)
  charge = 0
  charge += -1/(1+10**(pep_charges.c_term-pH))
  charge += -pep_charges.d_num/(1+10**(PkTable[:D][2]-pH))
  charge += -pep_charges.e_num/(1+10**(PkTable[:E][2]-pH))
  charge += -pep_charges.c_num/(1+10**(PkTable[:C][2]-pH))
  charge += -pep_charges.y_num/(1+10**(PkTable[:Y][2]-pH))
  charge += 1/(1+10**(pH - pep_charges.n_term))
  charge += pep_charges.h_num/(1+10**(pH-PkTable[:H][2]))
  charge += pep_charges.k_num/(1+10**(pH-PkTable[:K][2]))
  charge += pep_charges.r_num/(1+10**(pH-PkTable[:R][2]))
  charge
end

.identify_potential_charges(str) ⇒ Object 



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# File 'lib/charge_calculator.rb', line 7

def self.identify_potential_charges(str)
  string = str.upcase
  first = string[0]; last = string[-1]
  puts string if first.nil? or last.nil?
  begin
    out = PepCharges.new(string, PkTable[first.to_sym][0], PkTable[last.to_sym][1], 0, 0, 0 ,0 ,0 ,0, 0)
  rescue NoMethodError
    abort string
  end
  string.chars.each do |letter|
    case letter
      when "Y" 
        out.y_num += 1 
      when "C"
        out.c_num += 1
      when "K"
        out.k_num += 1 
      when "H"
        out.h_num += 1
      when "R"
        out.r_num += 1
      when "D"
        out.d_num += 1
      when "E"
        out.e_num += 1
    end
  end
  out
end