--- branches/new_design/OOPSE-2.0/src/primitives/Molecule.hpp	2004/11/01 22:52:57	1695
+++ branches/new_design/OOPSE-2.0/src/primitives/Molecule.hpp	2004/11/10 22:01:06	1725
@@ -38,13 +38,16 @@
 #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/Bond.hpp"
+//#include "primitives/Bend.hpp"
+//#include "primitives/Torsion.hpp"
+#include "primitives/SRI.hpp"
 #include "primitives/CutoffGroup.hpp"
 
 namespace oopse{
 
+class Constraint;
+
 /**
  * @class Molecule Molecule.hpp "primitives/Molecule.hpp"
  * @brief
@@ -52,7 +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();
 
         /**
@@ -70,14 +81,6 @@ 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 */
         void addAtom(Atom* atom);
@@ -135,6 +138,15 @@ class Molecule {
             return cutoffGroups_.size();
         }
 
+        /** Returns the total number of constraints in this 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
@@ -202,6 +214,10 @@ class Molecule {
          */        
         CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
 
+        Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
+
+        Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
+        
         //void setStampID( int info ) {stampID = info;} 
 
         void calcForces( void );
@@ -227,7 +243,7 @@ class Molecule {
         friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
         
     private:
-        int localIndex_;
+        
         int globalIndex_;
 
         std::vector<Atom*> atoms_;
@@ -237,6 +253,9 @@ class Molecule {
         std::vector<RigidBody*> rigidBodies_;
         std::vector<StuntDouble*> integrableObjects_;
         std::vector<CutoffGroup*> cutoffGroups_;
+        std::vector<Constraint*> constraints_;
+
+        int stampID;
 };
 
 } //namespace oopse