--- branches/mmeineke/mdtools/interface_implementation/SimSetup.cpp	2002/07/09 18:40:59	10
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2002/09/24 22:10:55	117
@@ -128,7 +128,7 @@ void SimSetup::createSim( void ){
   // create the atom and short range interaction arrays
   
   the_atoms = new Atom*[tot_atoms];
-  //  the_molecules = new Molecule[tot_nmol];
+  the_molecules = new Molecule[tot_nmol];
   
   
   if( tot_SRI ){
@@ -142,6 +142,7 @@ void SimSetup::createSim( void ){
   simnfo->sr_interactions = the_sris;
   simnfo->n_exclude = tot_SRI;
   simnfo->excludes = the_excludes;
+  
 
   // initialize the arrays
   
@@ -342,12 +343,17 @@ void SimSetup::makeAtoms( void ){
   double ux, uy, uz, uSqr, u;
   AtomStamp* current_atom;
   DirectionalAtom* dAtom;
+  int molIndex, molStart, molEnd, nMemb;
+  
 
+  molIndex = 0;
   index = 0;
   for( i=0; i<n_components; i++ ){
     
     for( j=0; j<components_nmol[i]; j++ ){
       
+      molStart = index;
+      nMemb = comp_stamps[i]->getNAtoms();
       for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
 	
 	current_atom = comp_stamps[i]->getAtom( k );
@@ -381,6 +387,13 @@ void SimSetup::makeAtoms( void ){
 	// increment the index and repeat;
 	index++;
       }
+      
+      molEnd = index -1;
+      the_molecules[molIndex].setNMembers( nMemb );
+      the_molecules[molIndex].setStartAtom( molStart );
+      the_molecules[molIndex].setEndAtom( molEnd );
+      molIndex++;
+
     }
   }
   
@@ -486,11 +499,6 @@ void SimSetup::makeMolecules( void ){
   the_ff->initializeTorsions( the_torsions );
 }
 
-void SimSetup::makeMolecules( void ){
-
-  //empy for now
-}
-
 void SimSetup::initFromBass( void ){
 
   int i, j, k;