Changes in src/Actions/FragmentationAction/FragmentationAction.cpp [be21fa:f10b0c]

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -45 +45 @@
 
   LOG(0, "STATUS: Fragmenting molecular system with current connection matrix maximum bond distance "
-      << params.distance << " up to "
-      << params.order << " order. Fragment files begin with "
-      << params.prefix << " and are stored as: "
-      << params.types << "." << std::endl);
+      << params.distance.get() << " up to "
+      << params.order.get() << " order. Fragment files begin with "
+      << params.prefix.get() << " and are stored as: "
+      << params.types.get() << "." << std::endl);
 
   DepthFirstSearchAnalysis DFS;
@@ -54 +54 @@
     mol = iter->second;
     ASSERT(mol != NULL, "No molecule has been picked for fragmentation.");
-    LOG(2, "INFO: Fragmenting molecule with bond distance " << params.distance << " angstroem, order of " << params.order << ".");
+    LOG(2, "INFO: Fragmenting molecule with bond distance " << params.distance.get() << " angstroem, order of " << params.order.get() << ".");
     start = clock();
     if (mol->hasBondStructure()) {
-      Fragmentation Fragmenter(mol, params.DoSaturation ? DoSaturate : DontSaturate);
-      Fragmenter.setOutputTypes(params.types);
-      ExitFlag = Fragmenter.FragmentMolecule(params.order, params.prefix, DFS);
+      Fragmentation Fragmenter(mol, params.DoSaturation.get() ? DoSaturate : DontSaturate);
+      Fragmenter.setOutputTypes(params.types.get());
+      ExitFlag = Fragmenter.FragmentMolecule(params.order.get(), params.prefix.get(), DFS);
     }
     World::getInstance().setExitFlag(ExitFlag);