Class: Mspire::Lipid::Modification

Inherits:
Object
  • Object
show all
Defined in:
lib/mspire/lipid/modification.rb

Overview

the convention is all mods are gains unless the name ends in an underscore

Constant Summary collapse

FORMULAS =

the charge on the mod should be represented by the number of plusses or minuses after the formula (Li+ for a 1 charge Lithium or H2+, 2 protons with a total of 2 charges)

{
  :proton => 'H',
  :ammonium => 'NH4',
  :lithium => 'Li',
  :sodium => 'Na',
  :water => 'H2O',
  :ammonia => 'NH3',
  :carbon_dioxide => 'CO2',
}
CHARGE = 
{
  :proton => 1,
  :ammonium => 1,
  :lithium => 1,
  :sodium=> 1,
  :water => 0,
  :ammonia => 0,
  :carbon_dioxide => 0,
}
MASSDIFFS =

determined by running formulas through Mspire::Mass.massdiff

{}

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(name, opts = {}) ⇒ Modification

if no mass or formula is given then it searches command mods for the name A number of opts are expected if they are not found in the FORMULAS, CHARGE, or MASSDIFFS hashes. However, the massdiff will be inferred from the formula if it is not given:

attributes:
:formula = the chemical formula, lipidmaps style ("C2H4BrO") or
           any valid argument to MolecularFormula.from_any
:massdiff = +/-Float
:charge = +/- Integer

instruction:
:loss = true   negates the mass diff sign and charge during initialization
               this option is typically only done for molecules
               already present in the FORMULA hash (e.g.)

proton_loss = Mspire::Lipid::Modification.new(:proton, :loss => true)
water_loss = Mspire::Lipid::Modification.new(:water, :loss => true)

Parameters:

  • name (Symbol) —

    the name of the mod



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# File 'lib/mspire/lipid/modification.rb', line 95

def initialize(name, opts={})
  @name = name
  @formula = 
    if ( form_string = (opts[:formula] || FORMULAS[name]) )
      Mspire::MolecularFormula.from_any( form_string )
    end
  @massdiff = opts[:massdiff] || MASSDIFFS[name]
  @charge = opts[:charge] || CHARGE[name]

  if opts[:loss]
    @charge = -@charge
    # necessary if you are using a named molecule and you want its loss
    # rather than gain (i.e., you want a negative massdiff)
    @massdiff = -@massdiff 
  end
end

Instance Attribute Details

#charge ⇒ Object

the charge



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# File 'lib/mspire/lipid/modification.rb', line 73

def charge
  @charge
end

#formula ⇒ Object

a MolecularFormula object



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# File 'lib/mspire/lipid/modification.rb', line 69

def formula
  @formula
end

#massdiff ⇒ Object

negative indicates a loss



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# File 'lib/mspire/lipid/modification.rb', line 71

def massdiff
  @massdiff
end

#name ⇒ Object

as a symbol



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# File 'lib/mspire/lipid/modification.rb', line 67

def name
  @name
end

Class Method Details

.formula_and_charge(string) ⇒ Object

given a string with a formula and charge, returns the formula portion and the charges (as a signed integer)



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# File 'lib/mspire/lipid/modification.rb', line 14

def self.formula_and_charge(string)
  md = string.match(/([^+]*)(\+*)$/)
  charges_string = md[2]
  if charges_string.nil?
    0
  else
    charges_string.count(charges_string[0])
    int = -int if charges_string[0] == '-'
  end
  [md[1], int]
end

.massdiff(formula, charge, gain = true) ⇒ Object

calculates the mass diff. For every positive charge the mass of an electron is subtracted; for every negative charge the mass of an electron is added. If gain is false, then the mass diff will be negative.



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# File 'lib/mspire/lipid/modification.rb', line 30

def self.massdiff(formula, charge, gain=true)
  Mspire::Mass.formula_to_exact_mass(formula)
  massdiff = Mspire::Mass.formula_to_exact_mass(formula)
  massdiff -= (charge * Mspire::Mass::ELECTRON) # + charge subtracts, - charge adds
  massdiff = -massdiff unless gain
  massdiff
end

Instance Method Details

#charged_formula_string ⇒ Object Also known as: to_s 



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# File 'lib/mspire/lipid/modification.rb', line 112

def charged_formula_string
  @formula.to_s + @charge.abs.times.map { (@charge > 0) ? '+' : '-' }.join
end

#gain? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mspire/lipid/modification.rb', line 118

def gain?
  massdiff > 0
end

#inspect ⇒ Object 



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# File 'lib/mspire/lipid/modification.rb', line 126

def inspect
  "<Mod: #{to_s}>"
end

#loss? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mspire/lipid/modification.rb', line 122

def loss?
  !gain?
end