atom.rb in rubabel-0.2.0

- old
+ new

@@ -77,11 +77,10 @@
         block.call _bond.upcast
         _bond = @ob.next_bond(iter)
       end
     end
 
-    alias_method :each, :each_bond
 
     # retrieves the bond 
     def get_bond(atom)
       @ob.get_bond(atom.ob).andand.upcast
     end
@@ -99,10 +98,11 @@
       while _atom
         block.call _atom.upcast
         _atom = @ob.next_nbr_atom(iter)
       end
     end
+    alias_method :each, :each_atom
 
     # returns the neighboring atoms.  Consider using each_atom.
     def atoms
       each_atom.map.to_a
     end
@@ -151,10 +151,83 @@
 
     def partial_charge
       @ob.get_partial_charge
     end
 
+    # permanently removes a hydrogen by properly incrementing the
+    # spin_multiplicity (and deleting a hydrogen if one is explicitly attached
+    # to the atom).  If called with cnt=2 a carbene or nitrene can be made
+    # (giving a spin_multiplicity of 3).  Makes no effort to ensure that the
+    # proper number of hydrogens already exist to be deleted, just alters the
+    # spin_multiplicity and deletes the right number of hydrogens if they are
+    # available to be deleted.  Adds one charge to the atom.
+    def remove_an_h!(add_charge=true)
+      new_spin = 
+        case @ob.get_spin_multiplicity
+        when 0 then 2
+        when 2 then 3
+        end
+      @ob.set_spin_multiplicity(new_spin)
+      atoms.each do |atom|
+        if atom.atomic_num == 1
+          self.mol.delete_atom(atom)
+          break
+        end
+      end
+      # add the charge
+      (self.charge = charge + 1) if add_charge
+      self
+    end
+
+    # philosophy on equality: there are *so* many ways for two atoms to be
+    # different that we can never really ensure that "equivalence" is met
+    # without calling ~20 methods.  We narrowly define equivalence so it is
+    # useful for that case and let the user make more complicated
+    # equivalency/equality definitions themselves.
+
+    # the exact same atom in the same molecule.  The equivalency test for
+    # molecules is a little pricey, so better to use something like atom.id ==
+    # other.id if you know you are working within the same molecule.
+    def equal?(other)
+      other.respond_to?(:mol) && mol.equal?(other.mol) && id == other.id 
+    end
+
+    alias_method :==, :equal?
+    alias_method :eql?, :equal?
+
+    ## opposite of remove_an_h!
+    ## THIS IS STILL BROKEN!!!
+    # maybe need to change the type?? C+ -> C2 or C3, but this gets really
+    # invasive...  Why is this so flippin hard to do!!
+    #def add_an_h!(remove_charge=true)
+      #new_spin = 
+        #case @ob.get_spin_multiplicity
+        #when 2 then 0
+        #when [1,3] then 2
+        #end
+      #@ob.set_spin_multiplicity(new_spin)
+      
+      #puts self.inspect_internals
+      #puts "EXAMIN B:"
+      #p self
+      #p self.charge
+      #(self.charge = self.charge - 1) if remove_charge
+      #puts "EXAMIN A:"
+      #puts self.inspect_internals
+      #p self
+      #p self.charge
+      #puts "BEFORE:"
+      #p mol.formula
+      #p mol.atoms
+      #mol.add_bond!(self, mol.add_atom!(1))
+      #puts "AFTER:"
+      #p mol.formula
+      #p mol.atoms
+      #abort 'here'
+      #self
+    #end
+
     def spin
       @ob.get_spin_multiplicity
     end
 
     def type
@@ -201,14 +274,31 @@
     def chiral_volume?() @ob.has_chiral_volume end
     def hbond_acceptor?() @ob.is_hbond_acceptor end
     def hbond_donor?() @ob.is_hbond_donor end
     def hbond_donor_h?() @ob.is_hbond_donor_h end
 
+    def double_bond?
+      each_bond.any? {|bond| bond.bond_order == 2 }
+    end
+
+    def single_bond?
+      each_bond.any? {|bond| bond.bond_order == 1 }
+    end
+
     def carboxyl_carbon?
-      atoms.any?(&:carboxyl_oxygen?)
+      each_atom.any?(&:carboxyl_oxygen?)
     end
 
+    def carbonyl_oxygen?
+      ats = atoms
+      ats.size == 1 && ats.first.el == :c && double_bond?
+    end
+
+    def carbonyl_carbon?
+      each_atom.any?(&:carbonyl_oxygen?)
+    end
+
 #    # does this carbon hold a primary alcohol
 #    def primary_alcohol_carbon?
 #    end
 
     def coords
@@ -216,7 +306,19 @@
     end
 
     def inspect
       "<#{type} id:#{id}>"
     end
+
+    def inspect_internals
+      "<" << @ob.methods.grep(/get_/).map do |mthd| 
+        begin
+          "#{mthd.to_s.sub(/get_/,'')}=#{@ob.send(mthd)}" 
+        rescue ArgumentError
+          nil
+        end
+      end.compact.join(" ") << ">"
+    end
+
+
   end
 end