--- trunk/OOPSE/libmdtools/Molecule.hpp	2003/03/21 17:42:12	378
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2003/03/27 19:21:42	422
@@ -3,32 +3,63 @@
 
 #include "Atom.hpp"
 #include "SRI.hpp"
+#include "MoleculeStamp.hpp"
+#include "Exclude.hpp"
 
+typedef struct{
+  
+  int stampID;   // the ID in the BASS component stamp array
+  int nAtoms;    // the number of atoms in the molecule
+  int nBonds;    // ... .. ..  . .bonds .. .. . . . . 
+  int nBends;    // . . . . .. . .bends . . . . .. . 
+  int nTorsions; // .. . . .. . . torsions . . .. . . 
+  int nOriented; // .. . . . .. . oriented atoms . . . 
+  
+  Atom** myAtoms;      // the array of atoms
+  Exclude** myExcludes;// the array of Excluded pairs 
+  Bond** myBonds;      // arrays of all the short range interactions
+  Bend** myBends;
+  Torsion** myTorsions;
+
+
+} molInit;
+
 class Molecule{
 
 public:
   
-  Molecule() {}
-  ~Molecule() {}
+  Molecule( void );
+  ~Molecule( void );
 
+  void initialize( molInit &theInit );
+
   int   getNMembers( void )  { return nMembers; }
   int   getStartAtom( void ) { return startAtom; }
   int   getEndAtom( void )   { return endAtom; }
   int   getStampID( void )   { return stampID; }
   
-  void   setNMembers( int info )  { nMembers = info; }
-  void   setStartAtom( int info ) { startAtom = info; }
-  void   setEndAtom( int info )   { endAtom = info; }
   void   setStampID( int info )   { stampID = info; }
   
 
 private:
 
+  int stampID;   // the ID in the BASS component stamp array
+  int nAtoms;    // the number of atoms in the molecule
+  int nBonds;    // ... .. ..  . .bonds .. .. . . . . 
+  int nBends;    // . . . . .. . .bends . . . . .. . 
+  int nTorsions; // .. . . .. . . torsions . . .. . . 
+  int nOriented; // .. . . . .. . oriented atoms . . . 
   int nMembers;
+
+  Atom** myAtoms;     // the array of atoms
+  Bond** myBonds;      // arrays of all the short range interactions
+  Bend** myBends;
+  Torsion** myTorsions;
+  
   int startAtom;
   int endAtom;
 
-  int stampID;
+
 };
 
 #endif