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

Methods inherited from Hash

#inverse

Constructor Details

#initialize(hash = {}, charge = 0) ⇒ MolecularFormula

Takes a hash and an optional Integer expressing the charge

{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 45

def initialize(hash={}, charge=0)
  @charge = charge
  self.merge!(hash)
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 41

def charge
  @charge
end

Class Method Details

.from_aaseq(aaseq) ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 8

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

.from_any(arg, charge = 0) ⇒ Object Also known as: []

arg may be a String, Hash, or MolecularFormula object.



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# File 'lib/mspire/molecular_formula.rb', line 28

def from_any(arg, charge=0)
  if arg.is_a?(String)
    from_string(arg, charge)
  else
    self.new(arg, arg.respond_to?(:charge) ? arg.charge : 0)
  end
end

.from_string(mol_form_str, charge = 0) ⇒ Object

takes a string, with properly capitalized elements making up the formula. The elements may be in any order.



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# File 'lib/mspire/molecular_formula.rb', line 19

def from_string(mol_form_str, charge=0)
  mf = self.new({}, charge)
  mol_form_str.scan(/([A-Z][a-z]?)(\d*)/).each do |k,v| 
    mf[k.downcase.to_sym] = (v == '' ? 1 : v.to_i)
  end
  mf
end

Instance Method Details

#*(int) ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 86

def *(int)
  self.dup.mul!(int)
end

#+(*others) ⇒ Object

returns a new formula object where all the atoms have been added up



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# File 'lib/mspire/molecular_formula.rb', line 51

def +(*others)
  self.dup.add!(*others)
end

#-(*others) ⇒ Object

returns a new formula object where all the formulas have been subtracted from the caller



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# File 'lib/mspire/molecular_formula.rb', line 66

def -(*others)
  self.dup.sub!(*others)
end

#/(int) ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 99

def /(int)
  self.dup.div!(int)
end

#==(other) ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 157

def ==(other)
  old_equal(other) && self.charge == other.charge
end

#add!(*others) ⇒ Object

returns self



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# File 'lib/mspire/molecular_formula.rb', line 56

def add!(*others)
  others.each do |other|
    self.merge!(other) {|key, oldval, newval| self[key] = oldval + newval }
    self.charge += other.charge
  end
  self
end

#avg_mass ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 126

def avg_mass
  inject(0.0) {|sum,(el,cnt)| sum + (Mspire::Mass::AVG[el]*cnt) }
end

#div!(int, also_do_charge = true) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/mspire/molecular_formula.rb', line 103

def div!(int, also_do_charge=true)
  raise ArgumentError, "must be an integer" unless int.is_a?(Integer)
  self.each do |k,v|
    quotient, modulus = v.divmod(int)
    raise ArgumentError "all numbers must be divisible by int" unless modulus == 0
    self[k] = quotient
  end
  if also_do_charge
    quotient, modulus = self.charge.divmod(int) 
    raise ArgumentError "charge must be divisible by int" unless modulus == 0
    self.charge = quotient
  end
  self
end

#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(consider_electron_masses = true) ⇒ Object

gives the monoisotopic mass adjusted by the current charge (i.e., adds/subtracts electron masses for the charges)



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# File 'lib/mspire/molecular_formula.rb', line 120

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

#mul!(int, also_do_charge = true) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/mspire/molecular_formula.rb', line 90

def mul!(int, also_do_charge=true)
  raise ArgumentError, "must be an integer" unless int.is_a?(Integer)
  self.each do |k,v|
    self[k] = v * int
  end
  self.charge *= int if also_do_charge
  self
end

#mz(consider_electron_masses = true) ⇒ Object

returns nil if the charge == 0



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# File 'lib/mspire/molecular_formula.rb', line 131

def mz(consider_electron_masses = true)
  if charge == 0
    nil
  else
    mass(consider_electron_masses) / charge
  end
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

#sub!(*others) ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 70

def sub!(*others)
  others.each do |other|
    oth = other.dup
    self.each do |k,v|
      if oth.key?(k)
        self[k] -= oth.delete(k)
      end
    end
    oth.each do |k,v|
      self[k] = -v
    end
    self.charge -= other.charge
  end
  self
end

#to_hash ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 151

def to_hash
  Hash[ self ]
end

#to_s(alphabetize = true) ⇒ Object 



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# File 'lib/mspire/molecular_formula.rb', line 139

def to_s(alphabetize=true)
  h = alphabetize ? self.sort : self
  st = ''
  h.each do |k,v|
    if v > 0
      st << k.to_s.capitalize
      st << v.to_s if v > 1
    end
  end 
  st
end