--- trunk/OOPSE/libmdtools/Molecule.hpp	2003/03/28 19:33:37	435
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2003/04/11 15:16:59	490
@@ -15,7 +15,7 @@ typedef struct{
   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
@@ -33,6 +33,12 @@ class Molecule{ (public)
   ~Molecule( void );
 
   void initialize( molInit &theInit );
+
+  void setMyIndex( int theIndex ){ myIndex = theIndex;}
+  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
+
+  int getMyIndex( void ) { return myIndex; }
+  int getGlobalIndex( void ) { return globalIndex; }
  
   int getNAtoms   ( void ) {return nAtoms;}
   int getNBonds   ( void ) {return nBonds;}
@@ -50,13 +56,19 @@ class Molecule{ (public)
   Exclude**  getMyExcludes( void ) {return myExcludes;}
   
   void setStampID( int info ) {stampID = info;}
+  
 
+
+
   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
@@ -68,6 +80,9 @@ class Molecule{ (public)
   int nMembers;  // .. . . . . . .atoms (legacy code) . . . 
   int nExcludes; // . . . . .. .. excludes .. . . 
 
+  int myIndex; // mostly just for debug (and for making pressure calcs work)
+  int globalIndex;
+
   Atom** myAtoms;     // the array of atoms
   Bond** myBonds;     // arrays of all the short range interactions
   Bend** myBends;