Class: Mspire::MolecularFormula

Inherits:
Hash
  • Object
show all
Defined in:
lib/mspire/molecular_formula.rb,
lib/mspire/isotope/distribution.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(arg, charge = 0) ⇒ MolecularFormula

takes a string or a hash:

"H22C12N1O3S2BeLi2"                    # <= order doesn't matter
{h: 22, c: 12, n: 1, o: 3, s: 2}  # case and string/sym doesn't matter



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# File 'lib/mspire/molecular_formula.rb', line 15

def initialize(arg, charge=0)
  @charge = charge
  if arg.is_a?(String)
    arg.scan(/([A-Z][a-z]?)(\d*)/).each do |k,v| 
      self[k.downcase.to_sym] = (v == '' ? 1 : v.to_i)
    end
  else
    self.merge!(arg)
  end
end

Instance Attribute Details

#charge ⇒ Object

integer desribing the charge state mass calculations will add/remove electron mass from this



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# File 'lib/mspire/molecular_formula.rb', line 10

def charge
  @charge
end

Class Method Details

.from_aaseq(aaseq) ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 26

def self.from_aaseq(aaseq)
  hash = aaseq.each_char.inject({}) do |hash,aa| 
    hash.merge(Mspire::Isotope::AA::ATOM_COUNTS[aa]) {|h,o,n| (o ? o : 0) +n }
  end
  hash[:h] += 2
  hash[:o] += 1
  self.new(hash)
end

Instance Method Details

#isotope_distribution(normalize = Mspire::Isotope::Distribution::NORMALIZE, percent_cutoff = nil) ⇒ Object

takes any element composition (see any_to_num_elements).

returns isotopic distribution beginning with monoisotopic peak. It cuts off when no more peaks contribute more than percent_cutoff to the total distribution. After that, normalization is performed.

all values will be fractional. normalize may be one of:

:total   normalize to the total intensity
:max     normalize to the highest peak intensity
:first   normalize to the intensity of the first peak 
        (this is typically the monoisotopic peak)



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# File 'lib/mspire/isotope/distribution.rb', line 32

def isotope_distribution(normalize=Mspire::Isotope::Distribution::NORMALIZE, percent_cutoff=nil)
  mono_dist = raw_isotope_distribution

  if percent_cutoff
    total_signal = mono_dist.reduce(:+)
    cutoff_index = (mono_dist.size-1).downto(0).find do |i|
      (mono_dist[i] / total_signal) >= (percent_cutoff/100.0)
    end
    # deletes these elements
    if cutoff_index
      mono_dist.slice!((cutoff_index+1)..-1)
    else
      # no peaks pass that percent cutoff threshold!
      mono_dist = []
    end
  end

  # normalization
  norm_by =
    case normalize
    when :total
      total_signal || mono_dist.reduce(:+)
    when :max
      mono_dist.max
    when :first
      mono_dist.first
    end
  mono_dist.map do |i| 
    v = i / norm_by
    (v > 0) ? v : 0
  end
end

#isotope_distribution_spectrum(*args) ⇒ Object

returns a spectrum object with mass values and intensity values. Arguments are passed directly to isotope_distribution. the molecule has a charge, this will be used to adjust the m/z values (by removing or adding electrons to the m/z and as the z)



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# File 'lib/mspire/isotope/distribution.rb', line 69

def isotope_distribution_spectrum(*args)
  intensities = isotope_distribution(*args)
  mono = self.map {|el,cnt| Mspire::Mass::MONO[el]*cnt }.reduce(:+)
  masses = Array.new(intensities.size)
  neutron = Mspire::Mass::NEUTRON
  masses[0] = mono
  (1...masses.size).each {|i| masses[i] = masses[i-1] + neutron }
  if self.charge && self.charge != 0
    masses.map! do |mass| 
      (mass - (self.charge * Mspire::Mass::ELECTRON)) / self.charge 
    end
  end
  Mspire::Spectrum.new [masses, intensities]
end

#mass ⇒ Object

gives the monoisotopic mass adjusted by the current charge



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# File 'lib/mspire/molecular_formula.rb', line 36

def mass
  mss = inject(0.0) {|sum,(el,cnt)| sum + (Mspire::Mass::MONO[el]*cnt) }
  mss - (Mspire::Mass::ELECTRON * charge)
end

#raw_isotope_distribution ⇒ Object

returns relative ratios from low nominal mass to high nominal mass. These are not normalized at all.



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# File 'lib/mspire/isotope/distribution.rb', line 86

def raw_isotope_distribution
  low_nominal = 0
  high_nominal = 0
  self.each do |el,cnt|
    isotopes = Mspire::Isotope::BY_ELEMENT[el]
    low_nominal += (isotopes.first.mass_number * cnt)
    high_nominal += (isotopes.last.mass_number * cnt)
  end

  ffts = self.map do |el, cnt|
    isotope_el_ar = NArray.float(high_nominal+1)
    Mspire::Isotope::BY_ELEMENT[el].each do |isotope|
      isotope_el_ar[isotope.mass_number] = isotope.relative_abundance
    end
    FFTW3.fft(isotope_el_ar)**cnt
  end
  FFTW3.ifft(ffts.reduce(:*)).real.to_a[low_nominal..high_nominal]
end