--- 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	2005/01/04 22:18:36	1901
@@ -35,13 +35,13 @@
 #include <vector>
 #include <iostream>
 
+#include "constraints/ConstraintPair.hpp"
 #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 +63,7 @@ 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();
 
         /**
@@ -75,6 +75,20 @@ class Molecule {
         }
 
         /**
+         * 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 +96,7 @@ class Molecule {
             return globalIndex_;
         }
 
+        
         /** add an atom into this molecule */
         void addAtom(Atom* atom);
 
@@ -98,8 +113,10 @@ class Molecule {
         void addRigidBody(RigidBody *rb);
 
         /** add a cutoff group into this molecule */
-        void addCutoffGroup(CutoffGroup* cp);         
+        void addCutoffGroup(CutoffGroup* cp);     
 
+        void addConstraintPair(ConstraintPair* consPair);
+
         /** */
         void complete();
 
@@ -139,8 +156,8 @@ class Molecule {
         }
 
         /** Returns the total number of constraints in this molecule */
-        unsigned int getNConstraints() {
-            return constraints_.size();
+        unsigned int getNConstraintPairs() {
+            return constraintPairs_.size();
         }
 
         Atom* getAtomAt(unsigned int i) {
@@ -214,19 +231,16 @@ class Molecule {
          */        
         CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
 
-        Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
+        ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i);
 
-        Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
+        ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::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();
 
+        /** get total mass of this molecule */        
+        double getMass();
 
         /** return the center of mass of this molecule */
         Vector3d getCom();
@@ -253,9 +267,10 @@ class Molecule {
         std::vector<RigidBody*> rigidBodies_;
         std::vector<StuntDouble*> integrableObjects_;
         std::vector<CutoffGroup*> cutoffGroups_;
-        std::vector<Constraint*> constraints_;
+        std::vector<ConstraintPair*> constraintPairs_;
 
-        int stampID;
+        int stampId_;
+        std::string moleculeName_;
 };
 
 } //namespace oopse