--- trunk/OOPSE/libmdtools/Molecule.hpp	2004/04/13 16:26:03	1104
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2004/05/11 20:33:41	1157
@@ -1,11 +1,17 @@
 #ifndef _MOLECULE_H_
 #define _MOLECULE_H_
 
+#include <set>
+#include <vector>
+
 #include "Atom.hpp"
 #include "SRI.hpp"
 #include "MoleculeStamp.hpp"
 #include "RigidBody.hpp"
+#include "CutoffGroup.hpp"
 
+using namespace std;
+
 typedef struct{
   
   int stampID;   // the ID in the BASS component stamp array
@@ -15,13 +21,15 @@ typedef struct{
   int nTorsions; // .. . . .. . . torsions . . .. . . 
   int nRigidBodies; // .. .. .. . rigid bodies ... .. 
   int nOriented; // .. . . . .. . oriented atoms . . . 
-
+  int nCutoffGroups;
+  
   Atom** myAtoms;      // the array of atoms
   Bond** myBonds;      // arrays of all the short range interactions
   Bend** myBends;
   Torsion** myTorsions;
   vector<RigidBody*>   myRigidBodies;
   vector<StuntDouble*> myIntegrableObjects;
+  vector<CutoffGroup*> myCutoffGroups;
 } molInit;
 
 class Molecule{
@@ -34,11 +42,11 @@ class Molecule{ (public)
   void initialize( molInit &theInit );
 
   void setMyIndex( int theIndex ){ myIndex = theIndex;}
-  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
-
   int getMyIndex( void ) { return myIndex; }
+
   int getGlobalIndex( void ) { return globalIndex; }
- 
+  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
+
   int getNAtoms   ( void )    {return nAtoms;}
   int getNBonds   ( void )    {return nBonds;}
   int getNBends   ( void )    {return nBends;}
@@ -53,6 +61,23 @@ class Molecule{ (public)
   Bend**      getMyBends   ( void )    {return myBends;}
   Torsion**   getMyTorsions( void )    {return myTorsions;}
   vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
+  vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
+
+  CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
+    i = myCutoffGroups.begin();
+    return i != myCutoffGroups.end()? *i : NULL;
+  }
+
+  CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
+    i++;
+    return i != myCutoffGroups.end()? *i : NULL;
+  }
+
+  bool belongToCutoffGroup(int index){
+    return cutoffAtomSet.find(index) != cutoffAtomSet.end()? true: false;
+  }
+
+  int getNCutoffGroups() {return nCutoffGroups;}
   
   void setStampID( int info ) {stampID = info;} 
 
@@ -78,7 +103,8 @@ class Molecule{ (public)
   int nRigidBodies; // .. . . .. .rigid bodies . . .. . . 
   int nOriented; // .. . . . .. . oriented atoms . . . 
   int nMembers;  // .. . . . . . .atoms (legacy code) . . . 
-
+  int nCutoffGroups;
+  
   int myIndex; // mostly just for debug (and for making pressure calcs work)
   int globalIndex;
 
@@ -88,7 +114,10 @@ class Molecule{ (public)
   Torsion** myTorsions;
   vector<RigidBody*>   myRigidBodies;
   vector<StuntDouble*> myIntegrableObjects;
+  vector<CutoffGroup*> myCutoffGroups;
+  set<int> cutoffAtomSet;  //global index of atoms belonging to cutoff group
 
+
 };
 
 #endif