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-              rf0674a
+              rdadc74
 #include <vector>
-#include "graph.hpp"
 class atom;
 class bond;
+class KeySet;
 class BondsPerShortestPath

src/Fragmentation/Fragmentation.cpp

rf0674a	rdadc74
29	29	#include "Element/periodentafel.hpp"
30	30	#include "Fragmentation/fragmentation_helpers.hpp"
	31	#include "Fragmentation/Graph.hpp"
31	32	#include "Fragmentation/KeySet.hpp"
32	33	#include "Fragmentation/PowerSetGenerator.hpp"

src/Fragmentation/Fragmentation.hpp

-              rf0674a
+              rdadc74
 #include <string>
-#include "graph.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
+#include "graph.hpp"
 class atom;
+class Graph;
 class KeySet;
 class molecule;

src/Fragmentation/Makefile.am

-              rf0674a
+              rdadc74
         Fragmentation/Fragmentation.cpp \
         Fragmentation/fragmentation_helpers.cpp \
+        Fragmentation/Graph.cpp \
         Fragmentation/helpers.cpp \
         Fragmentation/HessianMatrix.cpp \
 …
         Fragmentation/Fragmentation.hpp \
         Fragmentation/fragmentation_helpers.hpp \
+        Fragmentation/Graph.hpp \
+        Fragmentation/helpers.cpp \
         Fragmentation/helpers.hpp \
         Fragmentation/HessianMatrix.hpp \

src/Fragmentation/PowerSetGenerator.hpp

-              rf0674a
+              rdadc74
 #include "Fragmentation/BondsPerShortestPath.hpp"
-#include "graph.hpp"
 class bond;
 class UniqueFragment;
+class UniqueFragments;
 class PowerSetGenerator

src/Fragmentation/UniqueFragments.cpp

rf0674a	rdadc74
27	27	#include "Bond/bond.hpp"
28	28	#include "Element/element.hpp"
	29	#include "Fragmentation/Graph.hpp"
29	30	#include "Fragmentation/KeySet.hpp"
30	31	#include "graph.hpp"

src/Fragmentation/UniqueFragments.hpp

-              rf0674a
+              rdadc74
 #include <vector>
-#include "graph.hpp"
 class atom;
 class bond;
 class config;
+class Graph;
+class KeySet;
 /** Structure containing all values in power set combination generation.

src/Fragmentation/fragmentation_helpers.cpp

-              rf0674a
+              rdadc74
 #include "Bond/bond.hpp"
 #include "Element/element.hpp"
+#include "Fragmentation/Graph.hpp"
 #include "Fragmentation/KeySet.hpp"
+#include "graph.hpp"
 #include "Helpers/defs.hpp"
 #include "Helpers/helpers.hpp"
 …
     for(int i=0;i<NumLevels;i++) {
       if (FragmentLowerOrdersList[RootNr][i] != NULL) {
         InsertGraphIntoGraph(*FragmentList, (*FragmentLowerOrdersList[RootNr][i]), &counter);
+        (*FragmentList).InsertGraph((*FragmentLowerOrdersList[RootNr][i]), &counter);
+      }
+    }

src/Fragmentation/fragmentation_helpers.hpp

rf0674a	rdadc74
22	22
23	23	class bond;
	24	class Graph;
	25	class KeySet;
24	26	class molecule;
25	27

src/graph.cpp

-              rf0674a
+              rdadc74
 //};
-/** Inserts each KeySet in \a graph2 into \a graph1.
- * \param *out output stream for debugging
- * \param graph1 first (dest) graph
- * \param graph2 second (source) graph
- * \param *counter keyset counter that gets increased
- */
-void InsertGraphIntoGraph(Graph &graph1, Graph &graph2, int *counter)
+{
-  GraphTestPair testGraphInsert;
-  for(Graph::iterator runner = graph2.begin(); runner != graph2.end(); runner++) {
-    testGraphInsert = graph1.insert(GraphPair ((*runner).first,pair<int,double>((*counter)++,((*runner).second).second)));  // store fragment number and current factor
-    if (testGraphInsert.second) {
-      DoLog(2) && (Log() << Verbose(2) << "KeySet " << (*counter)-1 << " successfully inserted." << endl);
-    } else {
-      DoLog(2) && (Log() << Verbose(2) << "KeySet " << (*counter)-1 << " failed to insert, present fragment is " << ((*(testGraphInsert.first)).second).first << endl);
-      ((*(testGraphInsert.first)).second).second += (*runner).second.second;
-      DoLog(2) && (Log() << Verbose(2) << "New factor is " << (*(testGraphInsert.first)).second.second << "." << endl);
+    }
+  }
-};

src/graph.hpp

-              rf0674a
+              rdadc74
 #include <deque>
 #include <map>
-#include <set>
-#include <list>
 /****************************************** forward declarations *****************************/
-class atom;
-class bond;
-class config;
-class molecule;
-class SubGraph;
-class Node;
-class Edge;
-class KeySet;
-class UniqueFragments;
 /********************************************** definitions *********************************/
 …
 typedef std::deque<int> KeyStack;
-typedef std::pair<int, double> NumberValuePair;
-typedef std::map <KeySet, NumberValuePair > Graph;
-typedef std::pair <KeySet, NumberValuePair > GraphPair;
-typedef std::pair<Graph::iterator, bool> GraphTestPair;
-/******************************** Some small functions and/or structures **********************************/
-//bool operator < (KeySet SubgraphA, KeySet SubgraphB);   //note: this declaration is important, otherwise normal < is used (producing wrong order)
-void InsertGraphIntoGraph(Graph &graph1, Graph &graph2, int *counter);  // Insert all KeySet's in a Graph into another Graph
-/********************************************** declarations *******************************/
-///** Graph class containing the graphs behind molecules.
-// */
-//class Graph
-//{
-//      NodeMap ListOfNodes;            //!< tree-list of all nodes in this graph
-//      EdgeMap ListOfEdges;            //!< tree-multi-list of all nodes, referenced to node id
-//};
-//
-///** Class describing subgraphs of the Class \a Graph.
-// * SubGraph has its own node and edge lists, however also a pointer to its father graph
-// * and hence access to its list as well.
-// */
-//class SubGraph : class Graph
-//{
-//      class Graph *FatherGraph;               //!< Graph whose subgraph we are
-//};
-//
-///** Class containing the nodes of a graph.
-// */
-//class Node
-//{
-//      int     id;                             //!< individual id of the node
-//      char *Name;             //!< Name of the node for pretty printing
-//};
-//
-///** Class containing egdes in a Graph strructure.
-// */
-//class Edge
-//{
-//      class Node *leftnode;           //!< pointer to first node
-//      class Node *atomnode;           //!< pointer to second node
-//};
 #endif /*GRAPH_HPP_*/

src/molecule.hpp

rf0674a	rdadc74
43	43	class element;
44	44	class ForceMatrix;
	45	class Graph;
45	46	class LinkedCell;
46	47	class molecule;

src/moleculelist.cpp

rf0674a	rdadc74
33	33	#include "config.hpp"
34	34	#include "Element/element.hpp"
	35	#include "Fragmentation/Graph.hpp"
35	36	#include "Fragmentation/KeySet.hpp"
36	37	#include "Graph/BondGraph.hpp"

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