--- trunk/OOPSE/libmdtools/Verlet.cpp	2003/03/21 17:42:12	378
+++ trunk/OOPSE/libmdtools/Verlet.cpp	2003/03/27 20:12:15	423
@@ -36,11 +36,11 @@ Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
   entry_plug = &info;
   myFF = the_ff;
 
-
+  
   c_natoms = info.n_atoms;
   c_atoms = info.atoms;
-  c_sr_interactions = info.sr_interactions;
-  c_n_SRI = info.n_SRI;
+  nMols = info.n_mol;
+  molecules = info.molecules;
   c_is_constrained = 0;
   c_box_x = info.box_x;
   c_box_y = info.box_y;
@@ -67,25 +67,65 @@ Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
 
   Constraint *temp_con;
   Constraint *dummy_plug;
-  temp_con = new Constraint[c_n_SRI];
+  temp_con = new Constraint[info.n_SRI];
 
   c_n_constrained = 0;
   int constrained = 0;
-  
-  for(int i = 0; i < c_n_SRI; i++){
+  SRI** theArray;
+  for(int i = 0; i < nMols; i++){
     
-    constrained = c_sr_interactions[i]->is_constrained();
-
-    if(constrained){
+    theArray = molecules[i].getMyBonds();
+    for(int j=0; j<molecules[i].getNbonds(); j++){
       
-      dummy_plug = c_sr_interactions[i]->get_constraint();
-      temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
-      temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
-      temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
+      constrained = theArray[j]->is_constrained();
+      
+      if(constrained){
+	
+	dummy_plug = theArray[j]->get_constraint();
+	temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
+	temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
+	temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
+	
+	c_n_constrained++;
+	constrained = 0;
+      }
+    }
 
-      c_n_constrained++;
-      constrained = 0;
+    theArray = molecules[i].getMyBends();
+    for(int j=0; j<molecules[i].getNbends(); j++){
+      
+      constrained = theArray[j]->is_constrained();
+      
+      if(constrained){
+	
+	dummy_plug = theArray[j]->get_constraint();
+	temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
+	temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
+	temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
+	
+	c_n_constrained++;
+	constrained = 0;
+      }
+    }
+
+    theArray = molecules[i].getMyTorsions();
+    for(int j=0; j<molecules[i].getNtorsions(); j++){
+      
+      constrained = theArray[j]->is_constrained();
+      
+      if(constrained){
+	
+	dummy_plug = theArray[j]->get_constraint();
+	temp_con[c_n_constrained].set_a( dummy_plug->get_a() );
+	temp_con[c_n_constrained].set_b( dummy_plug->get_b() );
+	temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() );
+	
+	c_n_constrained++;
+	constrained = 0;
+      }
     }
+
+
   }
 
   if(c_n_constrained > 0){
@@ -94,11 +134,11 @@ Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
     c_constrained_i = new int[c_n_constrained];
     c_constrained_j = new int[c_n_constrained];
     c_constrained_dsqr = new double[c_n_constrained];
-
+    
     for( int i = 0; i < c_n_constrained; i++){
       
       /* add 1 to the index for the fortran arrays. */
-
+      
       c_constrained_i[i] = temp_con[i].get_a() + 1;
       c_constrained_j[i] = temp_con[i].get_b() + 1;
       c_constrained_dsqr[i] = temp_con[i].get_dsqr();