Class: Diadem::Calculator

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

Defined Under Namespace

Classes: Info, Modification, Polynomial

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(element = :H, mass_number = 2, penetration_table = Enrichment::AA_TABLE, isotope_table = Mspire::Isotope::BY_ELEMENT, round = false) ⇒ Calculator

returns spectra objects. The isotope_table handed in will not be altered



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# File 'lib/diadem/calculator.rb', line 83

def initialize(element=:H, mass_number=2, penetration_table=Enrichment::AA_TABLE, isotope_table=Mspire::Isotope::BY_ELEMENT, round=false)
  @round = round
  @penetration_table, @element, @mass_number = penetration_table, element, mass_number
  @isotope_table = dup_isotope_table(isotope_table)
end

Class Method Details

.distributions_to_polynomials(enrichments, distributions, num = 5, degree = 2) ⇒ Object

related intensities



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# File 'lib/diadem/calculator.rb', line 75

def distributions_to_polynomials(enrichments, distributions, num=5, degree=2)
  distributions.map {|dist| dist.intensities[0,num] }.transpose.each_with_index.map do |ar, m|
    polyfit(enrichments, ar, degree)
  end
end

.enrich_isotope(isotopes, mass_number, fraction = 1.0) ⇒ Object

returns new isotopes, properly enriched.



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# File 'lib/diadem/calculator.rb', line 65

def enrich_isotope(isotopes, mass_number, fraction=1.0)
  new_isotopes = isotopes.map(&:dup)
  leftover_fraction = 1.0 - fraction
  new_isotopes.each {|isot| isot.relative_abundance *= leftover_fraction }
  isot_to_enrich = new_isotopes.find {|isot| isot.mass_number == mass_number }
  isot_to_enrich.relative_abundance += fraction
  new_isotopes
end

.polyfit(x, y, degree) ⇒ Object

from rosettacode.org/wiki/Polynomial_regression#Ruby. Returns a Polynomial object



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# File 'lib/diadem/calculator.rb', line 55

def polyfit(x, y, degree)
  x_data = x.map {|xi| (0..degree).map { |pow| (xi**pow).to_f } }

  mx = Matrix[*x_data]
  my = Matrix.column_vector(y)

  Diadem::Calculator::Polynomial.new( ((mx.t * mx).inv * mx.t * my).transpose.to_a[0] )
end

Instance Method Details

#calculate_formula(aaseq_with_mods, mods) ⇒ Object

returns [formula_adjusted_for_mods, aaseq_with_no_mods]



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# File 'lib/diadem/calculator.rb', line 105

def calculate_formula(aaseq_with_mods, mods)
  mods.group_by(&:char).each do |modchar, mod|
    aaseq_with_mods.each_char do |char|
      if char == modchar
      end
    end
  end


  Mspire::MolecularFormula.from_aaseq(aaseq)
end

#calculate_isotope_distributions(aaseq, enrichments, normalize_type: :total, mods: Diadem::Calculator::Modification::DEFAULT_MODS) ⇒ Object

Returns [distributions, info]. Interprets lowercase m as singly oxidized methionine.



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# File 'lib/diadem/calculator.rb', line 118

def calculate_isotope_distributions(aaseq, enrichments, normalize_type: :total, mods: Diadem::Calculator::Modification::DEFAULT_MODS)
  @info = Info.new
  pct_cutoff = nil

  mf = Mspire::MolecularFormula
  aaseq_up = aaseq
  subtract_formula = mf.new
  add_formula = mf.new
  matched_mods = []
  mods.each do |mod|
    delta_formula = mod.gain ? add_formula : subtract_formula
    aaseq_up = aaseq_up.gsub(mod.match) do |match|
      matched_mods << [match, mod]
      delta_formula.add!(mod.diff_formula)
      mod.match_block.call(match)
    end
  end
  @info.mods = matched_mods

  formula = mf.from_aaseq(aaseq_up)
  formula += add_formula
  formula -= subtract_formula
  @info.formula = formula

  max_pen_frac = max_penetration_fraction(aaseq_up, formula)

  orig_isotopes = @isotope_table[@element]

  distributions = enrichments.map do |enrich_frac|
    effective_fraction = max_pen_frac * enrich_frac
    @isotope_table[@element] = Diadem::Calculator.enrich_isotope(orig_isotopes, @mass_number, effective_fraction)
    spectrum = formula.isotope_distribution_spectrum(normalize_type, pct_cutoff, @isotope_table)
    @isotope_table[@element] = orig_isotopes
    @info.masses = spectrum.mzs unless @info.masses
    Diadem::Distribution.new( spectrum.intensities )
  end
  [distributions, @info]
end

#dup_isotope_table(table) ⇒ Object 



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# File 'lib/diadem/calculator.rb', line 89

def dup_isotope_table(table)
  table.each.with_object({}) do |(key,val), new_table|
    new_table[key] = val.map {|obj| obj.dup }
  end
end

#max_penetration_fraction(aaseq, formula) ⇒ Object 



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# File 'lib/diadem/calculator.rb', line 95

def max_penetration_fraction(aaseq, formula)
  penetration = aaseq.each_char.inject(0.0) do |sum, aa|
    sum + ( @penetration_table[aa] || 0.0 )
  end
  penetration = penetration.round if @round
  @info.penetration = penetration
  penetration.to_f / formula[@element]
end