--- trunk/OOPSE/libmdtools/Molecule.hpp	2004/04/28 22:34:02	1140
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2004/05/12 16:38:45	1167
@@ -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 +21,14 @@ typedef struct{
   int nTorsions; // .. . . .. . . torsions . . .. . . 
   int nRigidBodies; // .. .. .. . rigid bodies ... .. 
   int nOriented; // .. . . . .. . oriented atoms . . . 
-
+  
   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{
@@ -54,6 +61,18 @@ class Molecule{ (public)
   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;
+  }
+
+  int getNCutoffGroups() {return nCutoffGroups;}
   
   void setStampID( int info ) {stampID = info;} 
 
@@ -79,7 +98,8 @@ 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;
 
@@ -89,8 +109,8 @@ class Molecule{ (public)
   Torsion** myTorsions;
   vector<RigidBody*>   myRigidBodies;
   vector<StuntDouble*> myIntegrableObjects;
+  vector<CutoffGroup*> myCutoffGroups;
 
-  bool   hasMassRatio;
 
 };