--- trunk/OOPSE/libmdtools/Molecule.hpp	2003/03/27 20:12:15	423
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2003/04/03 20:19:50	446
@@ -14,6 +14,9 @@ typedef struct{
   int nBends;    // . . . . .. . .bends . . . . .. . 
   int nTorsions; // .. . . .. . . torsions . . .. . . 
   int nOriented; // .. . . . .. . oriented atoms . . . 
+  int nExcludes; // . . .. . . . .exclude pairs.. . . . 
+
+  double* COM;   // the location of the center of mass of the molecule
   
   Atom** myAtoms;      // the array of atoms
   Exclude** myExcludes;// the array of Excluded pairs 
@@ -32,6 +35,8 @@ class Molecule{ (public)
   ~Molecule( void );
 
   void initialize( molInit &theInit );
+
+  void setMyIndex( int theIndex ){ myIndex = theIndex;}
  
   int getNAtoms   ( void ) {return nAtoms;}
   int getNBonds   ( void ) {return nBonds;}
@@ -45,15 +50,19 @@ class Molecule{ (public)
   Atom**     getMyAtoms   ( void ) {return myAtoms;}
   Bond**     getMyBonds   ( void ) {return myBonds;}
   Bend**     getMyBends   ( void ) {return myBends;}
-  Torsions** getmyTorsions( void ) {return myTorsions;}
-  Exclude**  getmyExcludes( void ) {return myExcludes;}
+  Torsion**  getMyTorsions( void ) {return myTorsions;}
+  Exclude**  getMyExcludes( void ) {return myExcludes;}
   
   void setStampID( int info ) {stampID = info;}
 
   void calcForces( void );
   double getPotential( void );
   
+  void printMe( void );
 
+  double* getCOM();
+  void moveCOM(double* delta);
+
 private:
 
   int stampID;   // the ID in the BASS component stamp array
@@ -65,12 +74,15 @@ class Molecule{ (public)
   int nMembers;  // .. . . . . . .atoms (legacy code) . . . 
   int nExcludes; // . . . . .. .. excludes .. . . 
 
+  int myIndex; // mostly just for debug
+
   Atom** myAtoms;     // the array of atoms
   Bond** myBonds;     // arrays of all the short range interactions
   Bend** myBends;
   Torsion** myTorsions;
   Exclude** myExcludes; // array of the excluded pairs of long range forces
   
+  double* COM;
 };
 
 #endif