lib/rubabel/atom.rb in rubabel-0.2.1 vs lib/rubabel/atom.rb in rubabel-0.2.2

@@ -1,5 +1,7 @@
+#encoding: utf-8
+
 require 'matrix'
 require 'andand'
 
 require 'rubabel/bond'
 
@@ -182,11 +184,11 @@
         when 0 then 2
         when 2 then 3
         end
       @ob.set_spin_multiplicity(new_spin)
       atoms.each do |atom|
-        if atom.atomic_num == 1
+        if atom.hydrogen?
           self.mol.delete_atom(atom)
           break
         end
       end
       # add the charge
@@ -244,10 +246,14 @@
 
     def spin
       @ob.get_spin_multiplicity
     end
 
+    def spin=(val)
+      @ob.set_spin_multiplicity(val)
+    end
+
     def type
       @ob.get_type
     end
 
     def valence
@@ -289,9 +295,16 @@
     def chirality_specified?() @ob.has_chirality_specified end
     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
+
+    # the total number of hydrogens bonded to the atom (implicit + explicit)
+    def hydrogen_count
+      @ob.implicit_hydrogen_count + @ob.explicit_hydrogen_count
+    end
+
+    alias_method :num_h, :hydrogen_count
 
     def double_bond?
       each_bond.any? {|bond| bond.bond_order == 2 }
     end