--- 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	2004/11/24 20:55:03	1782
@@ -38,10 +38,9 @@
 #include "math/Vector3.hpp"
 #include "primitives/Atom.hpp"
 #include "primitives/RigidBody.hpp"
-//#include "primitives/Bond.hpp"
-//#include "primitives/Bend.hpp"
-//#include "primitives/Torsion.hpp"
-#include "primitives/SRI.hpp"
+#include "primitives/Bond.hpp"
+#include "primitives/Bend.hpp"
+#include "primitives/Torsion.hpp"
 #include "primitives/CutoffGroup.hpp"
 
 namespace oopse{
@@ -55,7 +54,15 @@ 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, const std::string& molName);
         virtual ~Molecule();
 
         /**
@@ -66,6 +73,20 @@ class Molecule {
             return globalIndex_;
         }
 
+        /**
+         * Returns the stamp id of this molecule
+         * @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
+         * stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
+         */
+        int getStampId() {
+            return stampId_;
+        }
+
+        /** Returns the name of the molecule */
+        std::string getType() {
+            return moleculeName_;
+        }
+        
         /**
          * Sets the global index of this molecule.
          * @param new global index to be set
@@ -73,15 +94,8 @@ 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 */
         void addAtom(Atom* atom);
 
@@ -142,7 +156,11 @@ 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
@@ -214,12 +232,7 @@ class Molecule {
 
         Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
         
-        //void setStampID( int info ) {stampID = info;} 
 
-        void calcForces( void );
-
-        void atoms2rigidBodies( void );
-
         /** return the total potential energy of short range interaction of this molecule */
         double getPotential();
 
@@ -239,7 +252,7 @@ class Molecule {
         friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
         
     private:
-        int localIndex_;
+        
         int globalIndex_;
 
         std::vector<Atom*> atoms_;
@@ -251,7 +264,8 @@ class Molecule {
         std::vector<CutoffGroup*> cutoffGroups_;
         std::vector<Constraint*> constraints_;
 
-        int stampID;
+        int stampId_;
+        std::string moleculeName_;
 };
 
 } //namespace oopse