--- trunk/OOPSE/libmdtools/Molecule.hpp	2003/03/27 20:36:16	424
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2003/04/08 12:44:18	475
@@ -14,7 +14,8 @@ typedef struct{
   int nBends;    // . . . . .. . .bends . . . . .. . 
   int nTorsions; // .. . . .. . . torsions . . .. . . 
   int nOriented; // .. . . . .. . oriented atoms . . . 
-  
+  int nExcludes; // . . .. . . . .exclude pairs.. . . . 
+
   Atom** myAtoms;      // the array of atoms
   Exclude** myExcludes;// the array of Excluded pairs 
   Bond** myBonds;      // arrays of all the short range interactions
@@ -32,6 +33,8 @@ 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;}
@@ -53,7 +56,12 @@ class Molecule{ (public)
   void calcForces( void );
   double getPotential( void );
   
+  void printMe( void );
 
+  void getCOM( double COM[3] );
+  void moveCOM( double delta[3] );
+  double getCOMvel( double COMvel[3] );
+
 private:
 
   int stampID;   // the ID in the BASS component stamp array
@@ -65,6 +73,8 @@ 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;