began work on fragment prediction

lib/mspire/lipid.rb

@@ -2,13 +2,13 @@
 module Mspire
   class Lipid
     def self.members
-      [:lm_id,:common_name,:systematic_name,:formula,:mass,:category,:main_class,:sub_class]
+      [:lm_id,:common_name,:systematic_name,:formula,:mass,:category,:main_class,:sub_class,:smiles]
     end
 
     members.each {|mem| attr_accessor mem }
 
     def initialize(*args)
-      (@lm_id,@common_name,@systematic_name,@formula,@mass,@category,@main_class,@sub_class) = args
+      (@lm_id,@common_name,@systematic_name,@formula,@mass,@category,@main_class,@sub_class,@smiles) = args
     end
 
     def inspect

lib/mspire/lipid/ion.rb

@@ -1,3 +1,4 @@
+require 'mspire/lipid/ion/fragment'
 
 module Mspire
   class Lipid
@@ -16,6 +17,14 @@ def initialize(lipid, mods=[])
         @mz = nil
       end
 
+      def charge
+        z = 0
+        @modifications.each do |mod|
+          z -= mod.charge
+        end
+        z
+      end
+
       def mz
         return @mz if @mz
         mass = @lipid.mass
@@ -34,6 +43,7 @@ def mz
       def inspect
         "<|| Ion mz=#{mz} #{lipid.inspect} + #{modifications.map(&:inspect).join(', ')} ||>"
       end
+
     end
   end
 end

lib/mspire/lipid/ion/fragment.rb

@@ -0,0 +1,70 @@
+
+module Mspire
+  class Lipid
+
+    # goes from 1 to 99
+    CHAIN_PREFIXES = {
+      'meth' => 1,
+      'eth' => 2,
+      'prop' => 3,
+      'but' => 4,
+      'pent' => 5,
+      'hex' => 6,
+      'hept' => 7,
+      'oct' => 8,
+      'non' => 9,
+      'dec' => 10,
+      'undec' => 11,
+      'dodec' => 12,
+      'tridec' => 13,
+      'tetradec' => 14,
+      'pentadec' => 15,
+      'hexadec' => 16,
+      'heptadec' => 17,
+      'octadec' => 18,
+      'nonadec' => 19,
+      'eicos' => 20,
+      'heneicos' => 21,
+      'docos' => 22,
+      'tricos' => 23,
+      'tetracos' => 24,
+      'pentacos' => 25,
+      'hexacos' => 26,
+      'heptacos' => 27,
+      'octacos' => 28,
+      'nonacos' => 29
+    }
+
+    consistent = { 
+      0 => '',
+      1 => 'hen',
+      2 => 'do',
+      3 => 'tri',
+      4 => 'tetra',
+      5 => 'penta',
+      6 => 'hexa',
+      7 => 'hepta',
+      8 => 'octa',
+      9 => 'nona',
+    }
+
+    (3..9).each do |tens_place|
+      (0..9).each do |ones_place| 
+        key = consistent[ones_place] + consistent[tens_place] + "cont"
+        CHAIN_PREFIXES[key] = 10*tens_place + ones_place
+      end
+    end
+
+    class Ion
+      module Fragment
+        # predicts the MS/MS fragments for this ion
+        def predict_fragment_mzs
+          lipid.smiles
+        end
+
+      end
+
+      include Fragment
+    end
+  end
+end

lib/mspire/lipid/modification.rb

@@ -84,9 +84,13 @@ def initialize(name, opts={})
         @formula = opts[:formula] || FORMULAS[name]
         @massdiff = opts[:massdiff] || MASSDIFFS[name]
         @charge = opts[:charge] || CHARGE[name]
-        # 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 if opts[:loss]
+
+        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
 
       def charged_formula

spec/mspire/lipid/ion_spec.rb

@@ -5,7 +5,15 @@
 require 'mspire/lipid/modification'
 require 'mspire/lipid/ion'
 
+module MSS
+  CO2 = ( %w(c o o).map {|e| Mspire::Mass::MONO[e] }.reduce(:+) )
+  H2O = Mspire::Mass::MONO['h2o']
+  PROTON_LOSS = Mspire::Lipid::Modification.new(:proton, :loss => true)
+end
+
+
 describe Mspire::Lipid::Ion do
+
   before do
     lipid = Mspire::Lipid.new
     lipid.mass = 300.2
@@ -20,4 +28,56 @@
     @plus2.mz.should be_within(1e5).of(142.101994085)
   end
 
+  describe 'predicting ms/ms fragments' do
+    describe 'predicting simple fatty acyls' do
+      xit 'hexadecanoic acid' do
+        lipid = Mspire::Lipid.new('LMFA01010001', 'Palmitic acid', 'hexadecanoic acid',	'C16H32O2', 256.24, 'Fatty Acyls [FA]', 'Fatty Acids and Conjugates [FA01]', 'Straight chain fatty acids [FA0101]')
+
+        ion = Mspire::Lipid::Ion.new(lipid, [MSS::PROTON_LOSS])
+        frags = [ion.mz - MSS::H2O]
+        frags << ion.mz - MSS::CO2
+        frags << ion.mz - (MSS::H2O + MSS::CO2)
+
+        mzs = ion.predict_fragment_mzs
+        mzs.should be_an(Array)
+        mzs.sort.should == frags.sort
+      end
+
+      it '11-methyl-9S-hydroxy-13E-hexadecenoic acid' do
+        lipid = Mspire::Lipid.new(nil, 'Made Up', '11-methyl-9S-hydroxy-13E-hexadecenoic acid',	'C17H32O3', 284.23514488492003, 'Fatty Acyls [FA]', 'Fatty Acids and Conjugates [FA01]', 'Branched fatty acids [FA0102]')
+        ion = Mspire::Lipid::Ion.new(lipid, [MSS::PROTON_LOSS])
+
+        # one water loss
+        frags = [ion.mz - MSS::H2O]
+
+        # two water loss
+        frags << (ion.mz - (2*MSS::H2O))
+
+        # CO2 loss
+        frags << (ion.mz - MSS::CO2)
+
+        # CO2 + H20 loss
+        frags << ion.mz - (MSS::H2O + MSS::CO2)
+
+        oh_frag_mass = 140.12011513268
+        frag1 = (ion.mz - oh_frag_mass)
+
+        frags << frag1 - MSS::H2O
+
+        frags << frag1 - MSS::CO2
+
+        frags << frag1 - (MSS::H2O + MSS::CO2)
+
+        mzs = ion.predict_fragment_mzs
+        p mzs
+        #mzs.sort.should == frags.sort
+      end
+
+    end
+
+    it 'predicts simple glycerophosopholipids' do
+    end
+
+  end
+
 end