--- trunk/OOPSE/libmdtools/Symplectic.cpp	2003/03/21 17:42:12	378
+++ trunk/OOPSE/libmdtools/Symplectic.cpp	2003/03/27 20:12:15	423
@@ -35,10 +35,9 @@ Symplectic::Symplectic( SimInfo* the_entry_plug, Force
   myFF = the_ff;
   isFirst = 1;
 
+  molecules = entry_plug->molecules;
+  nMols = entry_plug->n_mol;
 
-  srInteractions = entry_plug->sr_interactions;
-  nSRI           =           entry_plug->n_SRI;
-
   // give a little love back to the SimInfo object
   
   if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator;
@@ -51,6 +50,7 @@ Symplectic::Symplectic( SimInfo* the_entry_plug, Force
     mass[i] = entry_plug->atoms[i]->getMass();
   }
 
+  
  
   // check for constraints
 
@@ -58,24 +58,63 @@ Symplectic::Symplectic( SimInfo* the_entry_plug, Force
 
   Constraint *temp_con;
   Constraint *dummy_plug;
-  temp_con = new Constraint[nSRI];
+  temp_con = new Constraint[entry_plug->n_SRI];
   n_constrained = 0;
   int constrained = 0;
   
-  for(int i = 0; i < nSRI; i++){
+  SRI** theArray;
+  for(int i = 0; i < nMols; i++){
     
-    constrained = srInteractions[i]->is_constrained();
-    
-    if(constrained){
+    theArray = molecules[i].getMyBonds();
+    for(int j=0; j<molecules[i].getNbonds(); j++){
       
-      dummy_plug = srInteractions[i]->get_constraint();
-      temp_con[n_constrained].set_a( dummy_plug->get_a() );
-      temp_con[n_constrained].set_b( dummy_plug->get_b() );
-      temp_con[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;
+      }
+    }
 
-      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(n_constrained > 0){