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-              rdcbb5d
+              rb4f72c
+ *
  * @param _graph instance of Graph containing keyset of each fragment
  * @param _mol molecule as reference
  */
 ExportGraph_ToFiles::ExportGraph_ToFiles(const Graph &_graph, molecule *&_mol, const enum HydrogenSaturation _saturation) :
+ * @param saturation whether to saturate dangling bonds with hydrogen or not
+ */
+ExportGraph_ToFiles::ExportGraph_ToFiles(const Graph &_graph, const enum HydrogenSaturation _saturation) :
                 ExportGraph(_graph),
-                mol(_mol),
                 BondFragments(World::getPointer()),
                 saturation(_saturation)
 …
   // store force index reference file
+  {
     SortIndex_t SortIndex(mol);
+    SortIndex_t SortIndex;
     BondFragments.StoreForcesFile(prefix, SortIndex);
+  }
 …
   // store keysets file
   TotalGraph.StoreKeySetFile(prefix);
+  {
-    // store Adjacency file
-    std::string filename = prefix + ADJACENCYFILE;
-    mol->StoreAdjacencyToFile(filename);
+  }
   // store Hydrogen saturation correction file
 …
     LOG(2, "DEBUG: Fragment No." << (*runner).second.first << " with TEFactor "
                 << (*runner).second.second << ".");
     BondFragments.insert(StoreFragmentFromKeySet(mol, test, World::getInstance().getConfig()));
+    BondFragments.insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
     ++count;
+  }
 …
  * First creates the minimal set of atoms from the KeySet, then creates the bond structure from the complete
  * molecule and adds missing hydrogen where bonds were cut.
- * \param *mol reference molecule
  * \param &Leaflet pointer to KeySet structure
  * \param IsAngstroem whether we have Ansgtroem or bohrradius
  * \return pointer to constructed molecule
  */
 molecule * ExportGraph_ToFiles::StoreFragmentFromKeySet(molecule *mol, KeySet &Leaflet, bool IsAngstroem)
+molecule * ExportGraph_ToFiles::StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem)
+{
   Info info(__func__);
 …
   molecule *Leaf = World::getInstance().createMolecule();
   StoreFragmentFromKeySet_Init(mol, Leaf, Leaflet, SonList);
+  StoreFragmentFromKeySet_Init(Leaf, Leaflet, SonList);
   // create the bonds between all: Make it an induced subgraph and add hydrogen
 //  LOG(2, "Creating bonds from father graph (i.e. induced subgraph creation).");
   CreateInducedSubgraphOfFragment(mol, Leaf, SonList, IsAngstroem);
+  CreateInducedSubgraphOfFragment(Leaf, SonList, IsAngstroem);
   //Leaflet->Leaf->ScanForPeriodicCorrection(out);
 …
 /** Initializes some value for putting fragment of \a *mol into \a *Leaf.
- * \param *mol total molecule
  * \param *Leaf fragment molecule
  * \param &Leaflet pointer to KeySet structure
 …
  * \return number of atoms in fragment
  */
 int ExportGraph_ToFiles::StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
+int ExportGraph_ToFiles::StoreFragmentFromKeySet_Init(molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
+{
   atom *FatherOfRunner = NULL;
   // first create the minimal set of atoms from the KeySet
+  World &world = World::getInstance();
   int size = 0;
   for(KeySet::const_iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
     FatherOfRunner = mol->FindAtom((*runner));  // find the id
+    FatherOfRunner = world.getAtom(AtomById(*runner));  // find the id
     SonList.insert( std::make_pair(FatherOfRunner->getNr(), Leaf->AddCopyAtom(FatherOfRunner) ) );
     size++;
 …
 /** Creates an induced subgraph out of a fragmental key set, adding bonds and hydrogens (if treated specially).
- * \param *out output stream for debugging messages
- * \param *mol total molecule
  * \param *Leaf fragment molecule
  * \param IsAngstroem whether we have Ansgtroem or bohrradius
  * \param SonList list which atom of \a *Leaf is a son of which atom in \a *mol
  */
 void ExportGraph_ToFiles::CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
+ * \param SonList list which atom of \a *Leaf is another atom's son
+ */
+void ExportGraph_ToFiles::CreateInducedSubgraphOfFragment(molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
+{
   bool LonelyFlag = false;

src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp

-              rdcbb5d
+              rb4f72c
 class ListOfLocalAtoms_t;
+class molecule;
 /** ExportGraph_ToFiles implements an ExportGraph as storing all fragmentary
 …
+{
 public:
         ExportGraph_ToFiles(const Graph &_graph, molecule *&_mol, const enum HydrogenSaturation _saturation);
+        ExportGraph_ToFiles(const Graph &_graph, const enum HydrogenSaturation _saturation);
         virtual ~ExportGraph_ToFiles();
 …
         void prepareMolecule();
   molecule * StoreFragmentFromKeySet(molecule *mol, KeySet &Leaflet, bool IsAngstroem);
   int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
   void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);
+  molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
+  int StoreFragmentFromKeySet_Init(molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
+  void CreateInducedSubgraphOfFragment(molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);
 private:
-  //!> molecule as reference
-  molecule *mol;
   //!> internal list of created molecules
         MoleculeListClass BondFragments;

src/Fragmentation/Fragmentation.cpp

-              rdcbb5d
+              rb4f72c
   LOG(1, "STATUS: We have created " << TotalGraph.size() << " fragments.");
+  {
+    // store Adjacency file
+    std::string filename = prefix + ADJACENCYFILE;
+    mol->StoreAdjacencyToFile(filename);
+  }
   // store adaptive orders into file
   StoreOrderAtSiteFile(prefix);

src/Fragmentation/Graph.cpp

-              rdcbb5d
+              rb4f72c
  * \param *counter keyset counter that gets increased
  */
 void Graph::InsertGraph(Graph &graph, int *counter)
+void Graph::InsertGraph(const Graph &graph, int &counter)
+{
   GraphTestPair testGraphInsert;
   for(Graph::iterator runner = graph.begin(); runner != graph.end(); runner++) {
     testGraphInsert = insert(GraphPair ((*runner).first,pair<int,double>((*counter)++,((*runner).second).second)));  // store fragment number and current factor
+  for(Graph::const_iterator runner = graph.begin(); runner != graph.end(); runner++) {
+    testGraphInsert = insert(GraphPair ((*runner).first,pair<int,double>(++counter,((*runner).second).second)));  // store fragment number and current factor
     if (testGraphInsert.second) {
       LOG(2, "INFO: KeySet " << (*counter)-1 << " successfully inserted.");
+      LOG(2, "INFO: KeySet " << counter-1 << " successfully inserted.");
     } else {
       LOG(2, "INFO: KeySet " << (*counter)-1 << " failed to insert, present fragment is " << ((*(testGraphInsert.first)).second).first);
+      LOG(2, "INFO: KeySet " << counter-1 << " failed to insert, present fragment is " << ((*(testGraphInsert.first)).second).first);
       ((*(testGraphInsert.first)).second).second += (*runner).second.second;
       LOG(2, "INFO: New factor is " << (*(testGraphInsert.first)).second.second << ".");

src/Fragmentation/Graph.hpp

rdcbb5d	rb4f72c
30	30	~Graph();
31	31
32		void InsertGraph(Graph &graph, int *counter);
	32	void InsertGraph(const Graph &graph, int &counter);
33	33
34	34	bool ParseKeySetFile(std::string &path);

src/Fragmentation/SortIndex.cpp

-              rdcbb5d
+              rb4f72c
 {}
-/** Constructor for SortIndex from the internal numbering in a molecule.
+ *
- * \param *mol molecule to place in the internal index
- */
-SortIndex_t::SortIndex_t(const molecule *mol)
+{
-  int AtomNo = 0;
-  for(molecule::const_iterator iter=mol->begin();iter!=mol->end();++iter){
-#ifndef NDEBUG
-    std::pair<index_t::iterator, bool> inserter =
-#endif
-        index.insert( std::make_pair((*iter)->getNr(), AtomNo) );
-    ASSERT( inserter.second,
-        "SortIndex_t::SortIndex_t() - index "+toString((*iter)->getNr())+" already present.");
-    ++AtomNo;
+  }
+}
 int SortIndex_t::find(atomId_t id) const
+{
+  index_t::const_iterator iter = index.find(id);
+  if (iter == index.end())
+    return -1;
+  else
+    return iter->second;
+  return id;
+}

src/Fragmentation/SortIndex.hpp

rdcbb5d	rb4f72c
28	28	public:
29	29	SortIndex_t();
30		~~SortIndex_t(const molecule *mol);~~
31	30
32	31	int find(atomId_t id) const;

src/Fragmentation/fragmentation_helpers.cpp

rdcbb5d	rb4f72c
102	102	for(int i=0;i<NumLevels;i++) {
103	103	if (FragmentLowerOrdersList[RootNr][i] != NULL) {
104		FragmentList.InsertGraph((*FragmentLowerOrdersList[RootNr][i]), &counter);
	104	FragmentList.InsertGraph((*FragmentLowerOrdersList[RootNr][i]), counter);
105	105	}
106	106	}

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Changeset b4f72c for src/Fragmentation

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