--- branches/mmeineke/OOPSE/libmdtools/Molecule.hpp	2003/03/21 17:42:12	377
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2004/04/28 22:34:02	1140
@@ -3,32 +3,95 @@
 
 #include "Atom.hpp"
 #include "SRI.hpp"
+#include "MoleculeStamp.hpp"
+#include "RigidBody.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 nRigidBodies; // .. .. .. . rigid bodies ... .. 
+  int nOriented; // .. . . . .. . oriented atoms . . . 
+
+  Atom** myAtoms;      // the array of atoms
+  Bond** myBonds;      // arrays of all the short range interactions
+  Bend** myBends;
+  Torsion** myTorsions;
+  vector<RigidBody*>   myRigidBodies;
+  vector<StuntDouble*> myIntegrableObjects;
+} molInit;
+
 class Molecule{
 
 public:
   
-  Molecule() {}
-  ~Molecule() {}
+  Molecule( void );
+  ~Molecule( void );
 
-  int   getNMembers( void )  { return nMembers; }
-  int   getStartAtom( void ) { return startAtom; }
-  int   getEndAtom( void )   { return endAtom; }
-  int   getStampID( void )   { return stampID; }
+  void initialize( molInit &theInit );
+
+  void setMyIndex( int theIndex ){ myIndex = theIndex;}
+  int getMyIndex( void ) { return myIndex; }
+
+  int getGlobalIndex( void ) { return globalIndex; }
+  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
+
+  int getNAtoms   ( void )    {return nAtoms;}
+  int getNBonds   ( void )    {return nBonds;}
+  int getNBends   ( void )    {return nBends;}
+  int getNTorsions( void )    {return nTorsions;}
+  int getNRigidBodies( void ) {return myRigidBodies.size();}
+  int getNOriented( void )    {return nOriented;}
+  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;}
+  vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
+  vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
   
-  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 );
+  void atoms2rigidBodies( void );
+  double getPotential( void );
   
+  void printMe( void );
 
+  void getCOM( double COM[3] );
+  void moveCOM( double delta[3] );
+  double getCOMvel( double COMvel[3] );
+  
+  double getTotalMass();
+
 private:
 
-  int nMembers;
-  int startAtom;
-  int endAtom;
+  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 nRigidBodies; // .. . . .. .rigid bodies . . .. . . 
+  int nOriented; // .. . . . .. . oriented atoms . . . 
+  int nMembers;  // .. . . . . . .atoms (legacy code) . . . 
 
-  int stampID;
+  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;
+  Torsion** myTorsions;
+  vector<RigidBody*>   myRigidBodies;
+  vector<StuntDouble*> myIntegrableObjects;
+
+  bool   hasMassRatio;
+
 };
 
 #endif