--- branches/new_design/OOPSE-2.0/src/primitives/Molecule.hpp	2004/11/10 22:01:06	1725
+++ 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{
@@ -63,7 +62,7 @@ class Molecule {
         typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
         typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;        
 
-        Molecule(int stampId, int globalIndex);
+        Molecule(int stampId, int globalIndex, const std::string& molName);
         virtual ~Molecule();
 
         /**
@@ -72,8 +71,22 @@ class Molecule {
          */
         int getGlobalIndex() {
             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
@@ -82,6 +95,7 @@ class Molecule {
             return globalIndex_;
         }
 
+        
         /** add an atom into this molecule */
         void addAtom(Atom* atom);
 
@@ -218,12 +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();
 
@@ -255,7 +264,8 @@ class Molecule {
         std::vector<CutoffGroup*> cutoffGroups_;
         std::vector<Constraint*> constraints_;
 
-        int stampID;
+        int stampId_;
+        std::string moleculeName_;
 };
 
 } //namespace oopse