Class: Bio::Sequence::AA

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

Constant Summary collapse

CHARGED_GROUPS = 
['K', 'R', 'H', 'D', 'E', 'C', 'Y']

Instance Method Summary collapse

Constructor Details

#initialize(sequence) ⇒ AA

Returns a new instance of AA.

Raises:

  • (ArgumentError) 


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# File 'lib/isoelectric_point/aa.rb', line 6

def initialize(sequence)
  raise ArgumentError.new("sequence is required") if sequence.nil? || sequence.strip == ''
  super(sequence.upcase.gsub(/\s/, ''))
end

Instance Method Details

#charge_at(ph, pka_name_or_set = 'dtaselect') ⇒ Object

Calculate the charge of the sequence at a given ph As a second argument you can pass the name of the PKA set or a custom PKA set



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# File 'lib/isoelectric_point/aa.rb', line 35

def charge_at(ph, pka_name_or_set = 'dtaselect')
  ['K', 'R', 'H'].inject(partial_charge(select_pka(pka_name_or_set)['N_TERMINUS'], ph)) do |memo, item|
    memo += partial_charge(select_pka(pka_name_or_set)[item], ph) * charged_residue_frequencies[item]
  end -
  ['D', 'E', 'C', 'Y'].inject(partial_charge(ph, select_pka(pka_name_or_set)['C_TERMINUS'])) do |memo, item|
    memo += partial_charge(ph, select_pka(pka_name_or_set)[item]) * charged_residue_frequencies[item]
  end
end

#isoelectric_point(pka_name_or_set = 'dtaselect', places = 2, loop_limit = 100) ⇒ Object

Calculate the Isoelectric Point pka_name_or_set: the name of a PKA set or a custom PKA set places: specify the number of decimal places the value should be rounded to. loop_limit: how many iterations should be made to find the point. You should not need to tweak this.



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# File 'lib/isoelectric_point/aa.rb', line 15

def isoelectric_point(pka_name_or_set = 'dtaselect', places = 2, loop_limit = 100)
  loops = 0
  ph = 7.5
  step = 3.5
  begin
    current_charge = charge_at(ph, pka_name_or_set)
    if current_charge > 0
      ph += step
    else
      ph -= step
    end
    step /= 2.0
    loops += 1
    raise "Could not find a result within #{loop_limit} loops using #{pka_name_or_set.inspect}" if loops == loop_limit
  end while not iep_reached?(current_charge)
  ph.round_to_places(places)
end