--- trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2005/01/12 22:41:40	246
+++ trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2005/03/09 17:30:29	413
@@ -54,6 +54,10 @@
 #include "visitors/RigidBodyVisitor.hpp"
 #include "visitors/OtherVisitor.hpp"
 #include "visitors/ZconsVisitor.hpp"
+#include "selection/SelectionEvaluator.hpp"
+#include "selection/SelectionManager.hpp"
+#include "visitors/LipidTransVisitor.hpp"
+
 using namespace oopse;
 
 int main(int argc, char* argv[]){
@@ -81,7 +85,7 @@ int main(int argc, char* argv[]){
   
   mdFileName = dumpFileName;
   mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
-  
+
   if (args_info.output_given){
     xyzFileName = args_info.output_arg;
   } else {
@@ -91,50 +95,24 @@ int main(int argc, char* argv[]){
   
   //parse md file and set up the system
   SimCreator creator;
-  SimInfo* info = creator.createSim(mdFileName);
+  SimInfo* info = creator.createSim(mdFileName, false);
   
   
   
   //creat visitor list
   CompositeVisitor* compositeVisitor = new CompositeVisitor();
-  
-  //creat ignore visitor
-  if(args_info.ignore_given ||args_info.water_flag){
     
-    IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
-    
-    for(int i = 0; i < args_info.ignore_given; i++)
-      ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
-    
-    //ignore water 
-    if(args_info.water_flag){
-      ignoreVisitor->addIgnoreType("SSD");
-      ignoreVisitor->addIgnoreType("SSD1");
-      ignoreVisitor->addIgnoreType("SSD_E");
-      ignoreVisitor->addIgnoreType("SSD_RF");
-      ignoreVisitor->addIgnoreType("TIP3P_RB_0");
-      ignoreVisitor->addIgnoreType("TIP4P_RB_0");
-      ignoreVisitor->addIgnoreType("TIP5P_RB_0");
-      ignoreVisitor->addIgnoreType("SPCE_RB_0");      
-      ignoreVisitor->addIgnoreType("DPD_RB_0");
-    }
-    
-    compositeVisitor->addVisitor(ignoreVisitor, 1000);
-  }
-  
   //creat RigidBody Visitor
   if(args_info.rigidbody_flag){
     RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
     compositeVisitor->addVisitor(rbCOMVisitor, 900);
   }
   
-  //compositeVisitor->addVisitor(lipidVisitor, 900);
-  
   //creat SSD atom visitor
   SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
   compositeVisitor->addVisitor(ssdVisitor, 800);
   
-  LinearVisitor* linearVisitor = new LinearAtomVisitor(info);
+  LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
   compositeVisitor->addVisitor(linearVisitor, 750);
   
   //creat default atom visitor
@@ -165,16 +143,30 @@ int main(int argc, char* argv[]){
     WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
     compositeVisitor->addVisitor(wrappingVisitor, 400);
   }
-  
+
   //creat replicate visitor
   if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
     Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
     ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
     compositeVisitor->addVisitor(replicateVisitor, 300);
   }
-  
+
+
+  //create rotation visitor
+  if (args_info.refsele_given&& args_info.originsele_given) {
+    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250); 
+  } else if (args_info.refsele_given || args_info.originsele_given) {
+    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
+    exit(1);
+  }
+    
   //creat xyzVisitor
-  XYZVisitor* xyzVisitor = new XYZVisitor(info);
+  XYZVisitor* xyzVisitor;
+  if (args_info.selection_given) {
+    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
+  } else {
+    xyzVisitor = new XYZVisitor(info);
+  }
   compositeVisitor->addVisitor(xyzVisitor, 200);
   
   std::cout << compositeVisitor->toString();
@@ -197,7 +189,7 @@ int main(int argc, char* argv[]){
   Molecule* mol;
   StuntDouble* integrableObject;
   RigidBody* rb;
-  
+       
   for (int i = 0; i < nframes; i += args_info.frame_arg){
     dumpReader->readFrame(i);
     
@@ -220,7 +212,8 @@ int main(int argc, char* argv[]){
     
     //update visitor
     compositeVisitor->update();
-    
+
+
     //visit stuntdouble
     for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
       for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;