--- trunk/src/brains/SimInfo.hpp	2004/09/24 04:16:43	2
+++ trunk/src/brains/SimInfo.hpp	2004/10/22 22:54:01	143
@@ -5,24 +5,23 @@
 #include <string>
 #include <vector>
 
-#include "Atom.hpp"
-#include "RigidBody.hpp"
-#include "Molecule.hpp"
-#include "Exclude.hpp"
-#include "SkipList.hpp"
-#include "AbstractClasses.hpp"
-#include "MakeStamps.hpp"
-#include "SimState.hpp"
-#include "Restraints.hpp"
+#include "primitives/Atom.hpp"
+#include "primitives/RigidBody.hpp"
+#include "primitives/Molecule.hpp"
+#include "brains/Exclude.hpp"
+#include "brains/SkipList.hpp"
+#include "primitives/AbstractClasses.hpp"
+#include "types/MakeStamps.hpp"
+#include "brains/SimState.hpp"
+#include "restraints/Restraints.hpp"
 
 #define __C
-#include "fSimulation.h"
-#include "fortranWrapDefines.hpp"
-#include "GenericData.hpp"
+#include "brains/fSimulation.h"
+#include "utils/GenericData.hpp"
 
 
 //#include "Minimizer.hpp"
-//#include "OOPSEMinimizer.hpp"
+//#include "minimizers/OOPSEMinimizer.hpp"
 
 
 double roundMe( double x );
@@ -89,13 +88,17 @@ class SimInfo{ (public)
 
   
   int usePBC; // whether we use periodic boundry conditions.
-  int useLJ; 
-  int useSticky;
+  int useDirectionalAtoms;
+  int useLennardJones; 
+  int useElectrostatics;
   int useCharges;
   int useDipoles;
-  int useReactionField;
-  int useGB;
+  int useSticky;
+  int useGayBerne;
   int useEAM;
+  int useShapes;
+  int useFLARB;
+  int useReactionField;
   bool haveCutoffGroups;
   bool useInitXSstate;
   double orthoTolerance;
@@ -152,13 +155,6 @@ class SimInfo{ (public)
 
   // sets the internal function pointer to fortran.
 
-  void setInternal( setFortranSim_TD fSetup,
-		    setFortranBox_TD fBox,
-		    notifyFortranCutOff_TD fCut){
-    setFsimulation = fSetup;
-    setFortranBoxSize = fBox;
-    notifyFortranCutOffs = fCut;
-  }
 
   int getNDF();
   int getNDFraw();
@@ -213,13 +209,7 @@ class SimInfo{ (public)
   void calcBoxL();
   double calcMaxCutOff();
 
-  // private function to initialize the fortran side of the simulation
-  setFortranSim_TD setFsimulation;
-
-  setFortranBox_TD setFortranBoxSize;
   
-  notifyFortranCutOff_TD notifyFortranCutOffs;
-  
   //Addtional Properties of SimInfo
   map<string, GenericData*> properties;
   void getFortranGroupArrays(SimInfo* info,