--- trunk/OOPSE/libmdtools/Molecule.hpp	2003/03/26 23:14:02	416
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2003/04/10 20:08:56	489
@@ -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
@@ -33,17 +34,43 @@ class Molecule{ (public)
 
   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 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;}
+  int getNBends   ( void ) {return nBends;}
+  int getNTorsions( void ) {return nTorsions;}
+  int getNOriented( void ) {return nOriented;}
+  int getNExcludes( void ) {return nExcludes;}
+  int getNMembers ( void ) {return nMembers;}
+  int getStampID  ( void ) {return stampID;}
+
+  Atom**     getMyAtoms   ( void ) {return myAtoms;}
+  Bond**     getMyBonds   ( void ) {return myBonds;}
+  Bend**     getMyBends   ( void ) {return myBends;}
+  Torsion**  getMyTorsions( void ) {return myTorsions;}
+  Exclude**  getMyExcludes( void ) {return myExcludes;}
   
-  void   setNMembers( int info )  { nMembers = info; }
-  void   setStartAtom( int info ) { startAtom = info; }
-  void   setEndAtom( int info )   { endAtom = info; }
-  void   setStampID( int info )   { stampID = info; }
+  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] );
+
+  void atomicRollCall(int* molMembership);
+
 private:
 
   int stampID;   // the ID in the BASS component stamp array
@@ -52,17 +79,18 @@ class Molecule{ (public)
   int nBends;    // . . . . .. . .bends . . . . .. . 
   int nTorsions; // .. . . .. . . torsions . . .. . . 
   int nOriented; // .. . . . .. . oriented atoms . . . 
-  int nMembers;
+  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
+  Bond** myBonds;     // arrays of all the short range interactions
   Bend** myBends;
   Torsion** myTorsions;
+  Exclude** myExcludes; // array of the excluded pairs of long range forces
   
-  int startAtom;
-  int endAtom;
-
-
 };
 
 #endif