fragmentable.rb in rubabel-0.2.0

- old
+ new

@@ -5,22 +5,24 @@
 module Rubabel
   class Molecule
     module Fragmentable
 
       #:sp3c_oxygen_asymmetric_far_sp3, :sp3c_nitrogen_asymmetric_far_sp3,
-      RULES = Set[ :alcohol_to_aldehyde, :peroxy_to_carboxy, :co2_loss, 
-        :sp3c_oxygen_double_bond_far_side_sp3, :sp3c_oxygen_double_bond_far_side_sp2, :sp3c_oxygen_double_bond_water_loss, :sp3c_nitrogen_double_bond,
-      ]
+      #RULES = Set[ :alcohol_to_aldehyde, :peroxy_to_carboxy, :co2_loss, 
+      #  :sp3c_oxygen_double_bond_far_side_sp3, :sp3c_oxygen_double_bond_far_side_sp2, :sp3c_oxygen_double_bond_water_loss, :sp3c_nitrogen_double_bond,
+      #]
       #ADDUCTS = [:lioh, :nh4cl, :nh4oh]
-      CO_RULES = Set[:alcohol_to_aldehyde, :peroxy_to_carboxy, :co2_loss, 
-        :sp3c_oxygen_double_bond_water_loss, :sp3c_oxygen_double_bond_far_side_sp2, :sp3c_oxygen_double_bond_far_side_sp3, :sp3c_oxygen_asymmetric_far_sp3
-      ]
+      #CO_RULES = Set[:alcohol_to_aldehyde, :peroxy_to_carboxy, :co2_loss, 
+      #  :sp3c_oxygen_double_bond_water_loss, :sp3c_oxygen_double_bond_far_side_sp2, :sp3c_oxygen_double_bond_far_side_sp3, :sp3c_oxygen_asymmetric_far_sp3
+      #]
 
+      RULES = Set[:cad_o, :cad_oo, :oxed_ether]
+
       DEFAULT_OPTIONS = {
         rules: RULES,
         #adduct: nil,
-        ph: 7.4,
+        #ph: 7.4,
         # return only the set of unique fragments
         uniq: false, 
       }
 
       # molecules and fragments should all have hydrogens added (add_h!)
@@ -140,115 +142,205 @@
           end
         end
 
       end
 
-      # to ensure proper fragmentation, will add_h!(ph) first at the given ph
+      # splits the molecule between the carbon and carbon_nbr, adds a double
+      # bond between the carbon and oxygen, and moves whatever was on the
+      # oxygen (e.g., an OH or a charge) to the carbon_nbr. Returns two new
+      # molecules.
+      def carbonyl_oxygen_dump(carbon, oxygen, carbon_nbr)
+        appendage = oxygen.atoms.find {|a| a.el != :c }
+        if oxygen.charge != 0
+          ocharge = oxygen.charge
+        end
+        nmol = self.dup
+        new_oxygen = nmol.atom(oxygen.id)
+        new_carbon = nmol.atom(carbon.id)
+        new_carbon_nbr = nmol.atom(carbon_nbr.id)
+        new_appendage = nmol.atom(appendage.id) if appendage
+        nmol.delete_bond(new_carbon.get_bond(new_carbon_nbr))
+        if new_appendage
+          nmol.delete_bond(new_oxygen.get_bond(new_appendage)) 
+          nmol.add_bond!(new_carbon_nbr, new_appendage)
+        end
+        if ocharge
+          new_carbon_nbr.charge += ocharge
+          new_oxygen.charge -= ocharge
+        end
+        new_carbon.get_bond(new_oxygen).bond_order = 2
+        nmol.split
+      end
+
+      # breaks the bond and gives the electrons to the oxygen
+      def carbon_oxygen_esteal(carbon, oxygen)
+        nmol = self.dup
+        nmol.ob.add_hydrogens
+        ncarbon = nmol.atom(carbon.id)
+        noxygen = nmol.atom(oxygen.id)
+        nmol.delete_bond(ncarbon, noxygen)
+        ncarbon.charge += 1
+        noxygen.charge -= 1
+        ncarbon.remove_an_h!
+        #p ncarbon.ob.implicit_hydrogen_count
+        #p ncarbon
+        #ncarbon.ob.decrement_implicit_valence
+        #p ncarbon.ob.implicit_hydrogen_count
+        #p ncarbon
+        #ncarbon.ob.increment_implicit_valence
+
+        nmol.title = nmol.to_s
+        p nmol.write("tmp.svg")
+        parts = nmol.split
+        p z=parts.first
+        p z.formula
+        p z.mass
+        p z.exact_mass
+        
+        puts "HIAY"
+      end
+
       # an empty array is returned if there are no fragments generated.
+      # Hydrogens are added at a pH of 7.4, unless they have already been
+      # added.
       #
-      #     :ph => 7.4
-      #     :uniq => false 
+      #     :rules => queryable by :include? set of rules
+      #     :uniq => false
       def fragment(opts={})
+        only_uniqs = true
         opts = DEFAULT_OPTIONS.merge(opts)
         opts[:rules].each do |rule| 
           raise ArgumentError, "bad rule: #{rule}" unless RULES.include?(rule)
         end
 
         had_hydrogens = self.h_added?
-
-        self.correct_for_ph!(opts[:ph])
+        self.correct_for_ph!(7.4) unless had_hydrogens
         self.remove_h!
 
-        rules = opts[:rules]
         fragment_sets = []
-        if rules.any? {|rule| CO_RULES.include?(rule) }
-          putsv "matching C-O"
-          self.each_match("CO").each do |_atoms|
-            # note: this will *not* match C=O
-            (carbon, oxygen) = _atoms
-            carbon_nbrs = carbon.atoms.reject {|atom| atom == oxygen }
-            c3_nbrs = carbon_nbrs.select {|atm| atm.type == 'C3' }
-            # pulling this out here causes it to work incorrectly internally
-            # (not sure why)
-            #co_bond = carbon.get_bond(oxygen)
 
-            case oxygen.bonds.size # non-hydrogen bonds
-            when 1  # *must* be an alcohol or a carboxylic acid
-              putsv "#{csmiles} oxygen has no other bonds besides C-O (alcohol or carboxylic acid)"
-              if carbon.type == 'C3'
-                if rules.include?(:sp3c_oxygen_double_bond_water_loss) 
-                  putsv "rule :sp3c_oxygen_double_bond_water_loss"
-                  fragment_sets.push *near_side_double_bond_break(carbon, oxygen)
-                end
-                if rules.include?(:alcohol_to_aldehyde)
-                    putsv "rule :alcohol_to_aldehyde"
-                  fragment_sets.push *alcohol_to_aldehyde(carbon, oxygen, carbon_nbrs)
-                end
-              elsif carbon.carboxyl_carbon?
-                if rules.include?(:co2_loss)
-                  putsv "rule :co2_loss"
-                  if c3_nbr = c3_nbrs.first
-                    fragment_sets.push *co2_loss(carbon, oxygen, c3_nbr)
-                  end
-                end
-              end
-            when 2
-              putsv "#{csmiles} c-o & oxygen has 2 non-hydrogen bonds"
-              oxygen_nbr = oxygen.atoms.reject {|atom| atom.idx == carbon.idx }.first
-              if carbon.type == 'C3'
-                if rules.include?(:peroxy_to_carboxy)
-                  fragment_sets.push *peroxy_to_carboxy(carbon, oxygen, carbon_nbrs, oxygen_nbr)
-                end
-                # ester and ethers (look *only* on close side for places to make
-                # double bond)
-
-                if oxygen_nbr.type == 'C3'
-                  putsv "oxygen nbr is C3"
-                  if rules.include?(:sp3c_oxygen_double_bond_far_side_sp3) 
-                    putsv "rule :sp3c_oxygen_double_bond_far_side_sp3"
-                    fragment_sets.push *near_side_double_bond_break(carbon, oxygen)
-                  end
-                  if rules.include?(:sp3c_oxygen_asymmetric_far_sp3)
-                    putsv "rule :sp3c_oxygen_asymmetric_far_sp3"
-                    # only returns a single frag set
-                    fragment_sets.push electrophile_snatches_electrons(carbon, oxygen)
-                  end
-                end
-                if oxygen_nbr.type == 'C2'
-                  if rules.include?(:sp3c_oxygen_double_bond_far_side_sp2)
-                    putsv "rule :sp3c_oxygen_double_bond_far_side_sp2"
-                    fragment_sets.push *near_side_double_bond_break(carbon, oxygen)
-                  end
-                end
-                # note: the case of a carboxy is found with CO search
-              end
+        if opts[:rules].any? {|r| [:cad_o, :cad_oo].include?(r) }
+          self.each_match("C[O;h1,O]", only_uniqs) do |carbon, oxygen|
+            carbon.atoms.select {|a| a.el == :c }.each do |carbon_nbr|
+              fragment_sets << carbonyl_oxygen_dump(carbon, oxygen, carbon_nbr)
             end
           end
         end
-        if rules.include?(:sp3c_nitrogen_double_bond)
-          self.each_match("CN") do |_atoms|
-            (carbon, nitrogen) = _atoms
-            num_nitrogen_bonds = nitrogen.bonds.size
-            case num_nitrogen_bonds
-            when 2
-              if carbon.type == 'C3'
-                fragment_sets.push *near_side_double_bond_break(carbon, nitrogen)
-              end
-            end
+        if opts[:rules].any? {|r| [:oxed_ether].include?(r) }
+          self.each_match("C[O&X2]", only_uniqs) do |carbon, oxygen|
+            fragment_sets << carbon_oxygen_esteal(carbon, oxygen)
           end
         end
 
         unless had_hydrogens
           fragment_sets.each {|set| set.each(&:remove_h!) }
           self.remove_h!
         end
         if opts[:uniq]
           # TODO: impelent properly
-          #fragment_sets = fragment_sets.uniq_by(&:csmiles) 
           raise NotImplementedError
+          #fragment_sets = fragment_sets.uniq_by(&:csmiles) 
         end
+
         fragment_sets
       end
+
+
+      #        had_hydrogens = self.h_added?
+
+      #self.correct_for_ph!(opts[:ph])
+      #self.remove_h!
+
+      #rules = opts[:rules]
+      #fragment_sets = []
+      #if rules.any? {|rule| CO_RULES.include?(rule) }
+      #putsv "matching C-O"
+      #self.each_match("CO").each do |_atoms|
+      ## note: this will *not* match C=O
+      #(carbon, oxygen) = _atoms
+      #carbon_nbrs = carbon.atoms.reject {|atom| atom == oxygen }
+      #c3_nbrs = carbon_nbrs.select {|atm| atm.type == 'C3' }
+      ## pulling this out here causes it to work incorrectly internally
+      ## (not sure why)
+      ##co_bond = carbon.get_bond(oxygen)
+
+      #case oxygen.bonds.size # non-hydrogen bonds
+      #when 1  # *must* be an alcohol or a carboxylic acid
+      #putsv "#{csmiles} oxygen has no other bonds besides C-O (alcohol or carboxylic acid)"
+      #if carbon.type == 'C3'
+      #if rules.include?(:sp3c_oxygen_double_bond_water_loss) 
+      #putsv "rule :sp3c_oxygen_double_bond_water_loss"
+      #fragment_sets.push *near_side_double_bond_break(carbon, oxygen)
+      #end
+      #if rules.include?(:alcohol_to_aldehyde)
+      #putsv "rule :alcohol_to_aldehyde"
+      #fragment_sets.push *alcohol_to_aldehyde(carbon, oxygen, carbon_nbrs)
+      #end
+      #elsif carbon.carboxyl_carbon?
+      #if rules.include?(:co2_loss)
+      #putsv "rule :co2_loss"
+      #if c3_nbr = c3_nbrs.first
+      #fragment_sets.push *co2_loss(carbon, oxygen, c3_nbr)
+      #end
+      #end
+      #end
+      #when 2
+      #putsv "#{csmiles} c-o & oxygen has 2 non-hydrogen bonds"
+      #oxygen_nbr = oxygen.atoms.reject {|atom| atom.idx == carbon.idx }.first
+      #if carbon.type == 'C3'
+      #if rules.include?(:peroxy_to_carboxy)
+      #fragment_sets.push *peroxy_to_carboxy(carbon, oxygen, carbon_nbrs, oxygen_nbr)
+      #end
+      ## ester and ethers (look *only* on close side for places to make
+      ## double bond)
+
+      #if oxygen_nbr.type == 'C3'
+      #putsv "oxygen nbr is C3"
+      #if rules.include?(:sp3c_oxygen_double_bond_far_side_sp3) 
+      #putsv "rule :sp3c_oxygen_double_bond_far_side_sp3"
+      #fragment_sets.push *near_side_double_bond_break(carbon, oxygen)
+      #end
+      #if rules.include?(:sp3c_oxygen_asymmetric_far_sp3)
+      #putsv "rule :sp3c_oxygen_asymmetric_far_sp3"
+      ## only returns a single frag set
+      #fragment_sets.push electrophile_snatches_electrons(carbon, oxygen)
+      #end
+      #end
+      #if oxygen_nbr.type == 'C2'
+      #if rules.include?(:sp3c_oxygen_double_bond_far_side_sp2)
+      #putsv "rule :sp3c_oxygen_double_bond_far_side_sp2"
+      #fragment_sets.push *near_side_double_bond_break(carbon, oxygen)
+      #end
+      #end
+      ## note: the case of a carboxy is found with CO search
+      #end
+      #end
+      #end
+      #end
+      #if rules.include?(:sp3c_nitrogen_double_bond)
+      #self.each_match("CN") do |_atoms|
+      #(carbon, nitrogen) = _atoms
+      #num_nitrogen_bonds = nitrogen.bonds.size
+      #case num_nitrogen_bonds
+      #when 2
+      #if carbon.type == 'C3'
+      #fragment_sets.push *near_side_double_bond_break(carbon, nitrogen)
+      #end
+      #end
+      #end
+      #end
+
+      #unless had_hydrogens
+      #fragment_sets.each {|set| set.each(&:remove_h!) }
+      #self.remove_h!
+      #end
+      #if opts[:uniq]
+      ## TODO: impelent properly
+      ##fragment_sets = fragment_sets.uniq_by(&:csmiles) 
+      #raise NotImplementedError
+      #end
+      #fragment_sets
+      #end
 
     end
     include Fragmentable
   end
 end