--- branches/new_design/OOPSE-2.0/src/primitives/Molecule.hpp	2004/11/05 02:56:22	1713
+++ branches/new_design/OOPSE-2.0/src/primitives/Molecule.hpp	2004/11/10 22:01:06	1725
@@ -55,7 +55,15 @@ class Molecule {
 class Molecule {
     public:
 
-        Molecule();
+        typedef std::vector<Atom*>::iterator AtomIterator;
+        typedef std::vector<Bond*>::iterator BondIterator;
+        typedef std::vector<Bend*>::iterator BendIterator;
+        typedef std::vector<Torsion*>::iterator TorsionIterator;
+        typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
+        typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
+        typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;        
+
+        Molecule(int stampId, int globalIndex);
         virtual ~Molecule();
 
         /**
@@ -72,14 +80,6 @@ class Molecule {
          */
         int setGlobalIndex(int index) {
             return globalIndex_;
-        }
-        
-        /** 
-         * Returns the local index of this molecule 
-         * @return the local index of this molecule
-         */
-        int getLocalIndex() {
-            return localIndex_;
         }
 
         /** add an atom into this molecule */
@@ -142,7 +142,11 @@ class Molecule {
         unsigned int getNConstraints() {
             return constraints_.size();
         }
-        
+
+        Atom* getAtomAt(unsigned int i) {
+            assert(i < atoms_.size());
+            return atoms_[i];
+        }
         /**
          * Returns the first atom in this molecule and initialize the iterator.
          * @return the first atom, return NULL if there is not cut off group in this molecule
@@ -239,7 +243,7 @@ class Molecule {
         friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
         
     private:
-        int localIndex_;
+        
         int globalIndex_;
 
         std::vector<Atom*> atoms_;