--- trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2006/05/23 18:46:11	968
+++ trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2008/07/30 18:11:19	1282
@@ -68,7 +68,6 @@ int main(int argc, char* argv[]){
   
   gengetopt_args_info args_info;
   std::string dumpFileName;
-  std::string mdFileName;
   std::string xyzFileName;
   
   //parse the command line option
@@ -84,9 +83,6 @@ int main(int argc, char* argv[]){
     exit(1);
   }
   
-  mdFileName = dumpFileName;
-  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
-
   if (args_info.output_given){
     xyzFileName = args_info.output_arg;
   } else {
@@ -96,10 +92,9 @@ int main(int argc, char* argv[]){
   
   //parse md file and set up the system
   SimCreator creator;
-  SimInfo* info = creator.createSim(mdFileName, false);
+  SimInfo* info = creator.createSim(dumpFileName, false);
   
-  
-  
+
   //create visitor list
   CompositeVisitor* compositeVisitor = new CompositeVisitor();
     
@@ -122,6 +117,12 @@ int main(int argc, char* argv[]){
   GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
   compositeVisitor->addVisitor(gbLipidVisitor, 740);
 
+  Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info);
+  compositeVisitor->addVisitor(ring5Visitor, 730);
+
+  HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info);
+  compositeVisitor->addVisitor(headVisitor, 720);
+
   //create default atom visitor
   DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
   compositeVisitor->addVisitor(defaultAtomVisitor, 700);
@@ -175,11 +176,18 @@ int main(int argc, char* argv[]){
     
   //create xyzVisitor
   XYZVisitor* xyzVisitor;
+
   if (args_info.selection_given) {
     xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
   } else {
     xyzVisitor = new XYZVisitor(info);
   }
+
+  if(args_info.printPosOnly_flag){
+    bool posOnly = true;
+    xyzVisitor->setPosOnly(posOnly);
+  }
+
   compositeVisitor->addVisitor(xyzVisitor, 200);
   
   std::cout << compositeVisitor->toString();
@@ -192,10 +200,8 @@ int main(int argc, char* argv[]){
   int nframes = dumpReader->getNFrames();
   
   
-  std::ofstream xyzStream;    
-  xyzStream .open(xyzFileName.c_str());
+  std::ofstream xyzStream(xyzFileName.c_str());
   
-  
   SimInfo::MoleculeIterator miter;
   Molecule::IntegrableObjectIterator  iiter;
   Molecule::RigidBodyIterator rbIter;
@@ -258,11 +264,10 @@ int main(int argc, char* argv[]){
     xyzVisitor->clear();
     
   }//end for (int i = 0; i < nframes; i += args_info.frame_arg)
-  
+ 
+  delete xyzVisitor; 
   xyzStream.close();
-  
   delete prepareVisitor; 
   delete compositeVisitor;
   delete info;
-   
 }