Changes in src/Actions/FragmentationAction/FragmentationAction.cpp [ce7fdc:07a47e]

File:

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

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -25 +25 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Fragmentation/Fragmentation.hpp"
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "molecule.hpp"
@@ -49 +51 @@
   getParametersfromValueStorage();
 
+  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);
+
   DepthFirstSearchAnalysis DFS;
   for (World::MoleculeSelectionConstIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
@@ -56 +64 @@
     start = clock();
     if (mol->hasBondStructure()) {
-      LOG(1, "STAUS: Fragmenting molecule with current connection matrix ...");
-      ExitFlag = mol->FragmentMolecule(params.order, params.path, DFS);
+      Fragmentation Fragmenter(mol, params.DoSaturation ? DoSaturate : DontSaturate);
+      Fragmenter.setOutputTypes(params.types);
+      ExitFlag = Fragmenter.FragmentMolecule(params.order, params.prefix, DFS);
     }
     World::getInstance().setExitFlag(ExitFlag);