Changes in src/Actions/FragmentationAction/FragmentationAction.cpp [112b09:623e89]

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -6 +6 @@
  */
 
-#include "Helpers/MemDebug.hpp"
-
 #include "Actions/FragmentationAction/FragmentationAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "config.hpp"
@@ -27 +24 @@
 #include "Actions/MapOfActions.hpp"
 
-const char FragmentationFragmentationAction::NAME[] = "subspace-dissect";
+const char FragmentationFragmentationAction::NAME[] = "fragment-mol";
 
 FragmentationFragmentationAction::FragmentationFragmentationAction() :
@@ -38 +35 @@
 Action::state_ptr FragmentationFragmentationAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
+  clock_t start,end;
+  molecule *mol = NULL;
+  double distance = -1.;
+  int order = 0;
+  config *configuration = World::getInstance().getConfig();
+  int ExitFlag = 0;
 
-  dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
+  cout << "pre-dialog"<< endl;
+  dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryDouble("distance", &distance, MapOfActions::getInstance().getDescription("distance"));
+  dialog->queryInt("order", &order, MapOfActions::getInstance().getDescription("order"));
 
   if(dialog->display()) {
+    cout << "POST-dialog"<< endl;
+    ASSERT(mol != NULL, "No molecule has been picked for fragmentation.");
+    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with bond distance " << distance << " angstroem, order of " << order << "." << endl);
+    DoLog(0) && (Log() << Verbose(0) << "Creating connection matrix..." << endl);
+    start = clock();
+    mol->CreateAdjacencyList(distance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
+    if (mol->hasBondStructure()) {
+      ExitFlag = mol->FragmentMolecule(order, configuration);
+    }
+    World::getInstance().setExitFlag(ExitFlag);
+    end = clock();
+    DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
     delete dialog;
     return Action::success;