Changeset c75363 for molecuilder/src/molecules.cpp

Timestamp:

May 2, 2008, 1:25:48 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

30fda2

Parents:

e936b3

Message:

HUGE REWRITE to allow for adaptive increase of the bond order, first working commit

Lots of code was thrown out:
-BottomUp, TopDown and GetAtomicFragments
-TEFactors are now used as "CreationCounters", i.e. the count how often a fragment as been created (ideal would be only once)
-ReduceToUniqueOnes and stuff all thrown out, since they are out-dated since use of hash table
Other changes:
-CreateListofUniqueFragments renamed to PowerSetGenerator
-PowerSetGenerator goes not over all reachable roots, but one given by calling function FragmentBOSSANOVA
-FragmentBOSSANOVA loops over all possible root sites and hands this over to PowerSetGenerator
-by the virtue of the hash table it is not important anymore whether created keysets are unique or not, as this is recognized in log(n). Hence, the label < label is not important anymore (and not applicable in an adaptive scheme with old, parsed keysets and unknown labels) (THIS IS HOWEVER NOT DONE YET!)
The setup is then as follows:

1. FragmentMolecule
   1. parses adjacency, keysets and orderatsite files
   2. performs DFS to find connected subgraphs (to leave this in was a design decision: might be useful later)
   3. a RootStack is created for every subgraph (here, later we implement the "update 10 sites with highest energy contribution", and that's why this consciously not done in the following loop)
   4. in a loop over all subgraphs

d1. calls FragmentBOSSANOVA with this RootStack and within the subgraph molecule structure
d2. creates molecule (fragment)s from the returned keysets (StoreFragmentFromKeySet)

5. combines the generated molecule lists from all subgraphs
6. saves to disk: fragment configs, adjacency, orderatsite, keyset files

2. FragmentBOSSANOVA
   1. constructs a complete keyset of the molecule
   2. In a loop over all possible roots from the given rootstack

b1. increases order of root site
b2. calls PowerSetGenerator with this order, the complete keyset and the rootkeynr
b3. for all consecutive lower levels PowerSetGenerator is called with the suborder, the higher order keyset as the restricted one and each site in the set as the root)
b4. these are merged into a fragment list of keysets

3. All fragment lists (for all orders, i.e. from all destination fields) are merged into one list for return

3. PowerSetGenerator
   1. initialises UniqueFragments structure
   2. fills edge list via BFS
   3. creates the fragment by calling recursive function SPFragmentGenerator with UniqueFragments structure, 0 as root distance, the edge set, its dimension and the current suborder
   4. Free'ing structure
4. SPFragmentGenerator (nothing much has changed here)
   1. loops over every possible combination (2^{dimension of edge set)}

a1. inserts current set, if there's still space left

a11. yes: calls SPFragmentGenerator with structure, created new edge list and size respective to root distance+1
a12. no: stores fragment into keyset list by calling InsertFragmentIntoGraph

a2. removes all items added into the snake stack (in UniqueFragments structure) added during level (root distance) and current set

File:

• molecuilder/src/molecules.cpp (modified) (34 diffs)

molecuilder/src/molecules.cpp

@@ -1898 +1898 @@
     return false;
   }
-  cout << Verbose(1) << "Parsing the KeySet file ... ";
+  cout << Verbose(1) << "Parsing the KeySet file ... " << endl;
   // open file and read
   sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, KEYSETFILE);
@@ -1942 +1942 @@
  * \return true - file written successfully, false - writing failed
  */
-bool molecule::StoreAdjacencyToFile(ofstream *out, char *path, int bondorder)
+bool molecule::StoreAdjacencyToFile(ofstream *out, char *path)
 {
   ofstream AdjacencyFile;
@@ -1953 +1953 @@
   cout << Verbose(1) << "Saving adjacency list ... ";
   if (AdjacencyFile != NULL) {
-    AdjacencyFile << "Order\t" << bondorder << endl;
     Walker = start;
     while(Walker->next != end) {
@@ -1977 +1976 @@
  * \param *path path to file
  * \param **ListOfAtoms allocated (molecule::AtomCount) and filled lookup table for ids (Atom::nr) to *Atom
- * \param bondorder check whether files matches desired bond order
  * \return true - structure is equal, false - not equivalence
  */ 
-bool molecule::CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms, int bondorder)
+bool molecule::CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms)
 {
   char *filename = (char *) Malloc(sizeof(char)*MAXSTRINGSIZE, "molecule::CheckAdjacencyFileAgainstMolecule - filename");
@@ -1995 +1993 @@
     int CurrentBondsOfAtom;
 
-    // determine order from file
-    File.getline(filename, MAXSTRINGSIZE);    
-    if (bondorder != atoi(&filename[5])) {
-      *out << "Bond order desired is " << bondorder << " and does not match one in file " << filename[6] << "." << endl;
-      status = false;
-    } else {
-      // Parse the file line by line and count the bonds
-      while (!File.eof()) {
-        File.getline(filename, MAXSTRINGSIZE);
-        stringstream line;
-        line.str(filename);
-        int AtomNr = -1;
-        line >> AtomNr;
-        CurrentBondsOfAtom = -1; // we count one too far due to line end
-        // parse into structure
-        if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
-          while (!line.eof())
-            line >> CurrentBonds[ ++CurrentBondsOfAtom ];
-          // compare against present bonds
-          //cout << Verbose(2) << "Walker is " << *Walker << ", bond partners: ";
-          if (CurrentBondsOfAtom == NumberOfBondsPerAtom[AtomNr]) {
-            for(int i=0;i<NumberOfBondsPerAtom[AtomNr];i++) {
-              int id = ListOfBondsPerAtom[AtomNr][i]->GetOtherAtom(ListOfAtoms[AtomNr])->nr;
-              int j = 0;
-              for (;(j<CurrentBondsOfAtom) && (CurrentBonds[j++] != id);); // check against all parsed bonds
-              if (CurrentBonds[j-1] != id) { // no match ? Then mark in ListOfAtoms
-                ListOfAtoms[AtomNr] = NULL;
-                NonMatchNumber++;
-                status = false;
-                //out << "[" << id << "]\t";
-              } else {
-                //out << id << "\t";
-              }
+    // Parse the file line by line and count the bonds
+    while (!File.eof()) {
+      File.getline(filename, MAXSTRINGSIZE);
+      stringstream line;
+      line.str(filename);
+      int AtomNr = -1;
+      line >> AtomNr;
+      CurrentBondsOfAtom = -1; // we count one too far due to line end
+      // parse into structure
+      if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
+        while (!line.eof())
+          line >> CurrentBonds[ ++CurrentBondsOfAtom ];
+        // compare against present bonds
+        //cout << Verbose(2) << "Walker is " << *Walker << ", bond partners: ";
+        if (CurrentBondsOfAtom == NumberOfBondsPerAtom[AtomNr]) {
+          for(int i=0;i<NumberOfBondsPerAtom[AtomNr];i++) {
+            int id = ListOfBondsPerAtom[AtomNr][i]->GetOtherAtom(ListOfAtoms[AtomNr])->nr;
+            int j = 0;
+            for (;(j<CurrentBondsOfAtom) && (CurrentBonds[j++] != id);); // check against all parsed bonds
+            if (CurrentBonds[j-1] != id) { // no match ? Then mark in ListOfAtoms
+              ListOfAtoms[AtomNr] = NULL;
+              NonMatchNumber++;
+              status = false;
+              //out << "[" << id << "]\t";
+            } else {
+              //out << id << "\t";
             }
-            //out << endl;
-          } else {
-            *out << "Number of bonds for Atom " << *ListOfAtoms[AtomNr] << " does not match, parsed " << CurrentBondsOfAtom << " against " << NumberOfBondsPerAtom[AtomNr] << "." << endl;
-            status = false;
           }
+          //out << endl;
+        } else {
+          *out << "Number of bonds for Atom " << *ListOfAtoms[AtomNr] << " does not match, parsed " << CurrentBondsOfAtom << " against " << NumberOfBondsPerAtom[AtomNr] << "." << endl;
+          status = false;
         }
       }
-      File.close();
-      File.clear();
-      if (status) { // if equal we parse the KeySetFile
-        *out << " done: Equal." << endl;
-        status = true;
-      } else
-        *out << " done: Not equal by " << NonMatchNumber << " atoms." << endl;
-    }
+    }
+    File.close();
+    File.clear();
+    if (status) { // if equal we parse the KeySetFile
+      *out << " done: Equal." << endl;
+      status = true;
+    } else
+      *out << " done: Not equal by " << NonMatchNumber << " atoms." << endl;
     Free((void **)&CurrentBonds, "molecule::CheckAdjacencyFileAgainstMolecule - **CurrentBonds");
   } else {
@@ -2057 +2048 @@
  * Writes for each fragment a config file.
  * \param *out output stream for debugging
- * \param BottomUpOrder up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
- * \param TopDownOrder up to how many neighbouring bonds a fragment contains in BondOrderScheme::TopDown scheme
- * \param Scheme which BondOrderScheme to use for the fragmentation
+ * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
  * \param *configuration configuration for writing config files for each fragment
- * \param CutCyclic whether to add cut cyclic bond or to saturate
- */
-void molecule::FragmentMolecule(ofstream *out, int BottomUpOrder, int TopDownOrder, enum BondOrderScheme Scheme, config *configuration, enum CutCyclicBond CutCyclic)
+ */
+void molecule::FragmentMolecule(ofstream *out, int Order, config *configuration)
 {
         MoleculeListClass **BondFragments = NULL;
@@ -2072 +2060 @@
   int AtomNo;
   int MinimumRingSize;
-  int TotalFragmentCounter = 0;
-  int FragmentCounter = 0;
+  int TotalFragmentCounter;
+  int FragmentCounter;
   MoleculeLeafClass *MolecularWalker = NULL;
   MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
   fstream File;
-  bool status = true;
-
-  cout << endl;
+  bool FragmentationToDo = true;
+
+  *out << endl;
 #ifdef ADDHYDROGEN
-  cout << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl;
+  *out << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl;
 #else
-  cout << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl;
+  *out << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl;
 #endif
 
@@ -2101 +2089 @@
   if (Walker->next != end) {  // everything went alright
     *out << " range of nuclear ids exceeded [0, AtomCount)." << endl;
-    status = false;
-  }
-  status = status && CheckAdjacencyFileAgainstMolecule(out, configuration->configpath, ListOfAtoms, BottomUpOrder); 
-  if (status) {  // NULL entries in ListOfAtoms contain NonMatches
-    status = status && ParseKeySetFile(out, configuration->configpath, ListOfAtoms, FragmentList, configuration->GetIsAngstroem());
-  }
+    FragmentationToDo = false;
+  }
+  FragmentationToDo = FragmentationToDo && CheckAdjacencyFileAgainstMolecule(out, configuration->configpath, ListOfAtoms); 
+  if (FragmentationToDo)  // NULL entries in ListOfAtoms contain NonMatches
+    FragmentationToDo = FragmentationToDo && ParseKeySetFile(out, configuration->configpath, ListOfAtoms, FragmentList, configuration->GetIsAngstroem());
+  if (FragmentationToDo)  // parse the adaptive order per atom/site/vertex
+    FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(out, configuration->configpath);
   Free((void **)&ListOfAtoms, "molecule::FragmentMolecule - **ListOfAtoms");
 
   // =================================== Begin of FRAGMENTATION ===============================
-  if (!status) {
-    // === store Adjacency file ===
-    StoreAdjacencyToFile(out, configuration->configpath, BottomUpOrder);
-
+  if (FragmentationToDo) { // if we parsed Adjacancy, check whether OrderAtSite is above Order everywhere
+    Walker = start;
+    while (Walker->next != end) { // create a lookup table (Atom::nr -> atom) used as a marker table lateron 
+      Walker = Walker->next;
+#ifdef ADDHYDROGEN
+      if (Walker->type->Z != 1) // skip hydrogen
+#endif
+        if (Walker->AdaptiveOrder < Order)
+          FragmentationToDo = false;
+    }
+  } 
+  
+  if (!FragmentationToDo) { // if we have still do something, FragmentationToDo will be false
     // === first perform a DFS analysis to gather info on cyclic structure and a list of disconnected subgraphs ===
-    Subgraphs = DepthFirstSearchAnalysis((ofstream *)&cout, false, MinimumRingSize);
+    Subgraphs = DepthFirstSearchAnalysis((ofstream *)&*out, false, MinimumRingSize);
     MolecularWalker = Subgraphs;
     // fill the bond structure of the individually stored subgraphs
     while (MolecularWalker->next != NULL) {
       MolecularWalker = MolecularWalker->next;
-      cout << Verbose(1) << "Creating adjacency list for subgraph " << MolecularWalker << "." << endl;
-      MolecularWalker->Leaf->CreateAdjacencyList((ofstream *)&cout, BondDistance);
-      MolecularWalker->Leaf->CreateListOfBondsPerAtom((ofstream *)&cout);
+      *out << Verbose(1) << "Creating adjacency list for subgraph " << MolecularWalker << "." << endl;
+      MolecularWalker->Leaf->CreateAdjacencyList(out, BondDistance);
+      MolecularWalker->Leaf->CreateListOfBondsPerAtom(out);
     }
     
     // === fragment all subgraphs ===
-    if ((MinimumRingSize != -1) && ((BottomUpOrder >= MinimumRingSize) || (TopDownOrder >= MinimumRingSize))) {
-      cout << Verbose(0) << "Bond order greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed." << endl;
+    if ((MinimumRingSize != -1) && (Order >= MinimumRingSize)) {
+      *out << Verbose(0) << "Bond order greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed." << endl;
     } else {
       FragmentCounter = 0;
       MolecularWalker = Subgraphs;
-      // count subgraphs
+      // count subgraphs and allocate fragments
       while (MolecularWalker->next != NULL) {
         MolecularWalker = MolecularWalker->next;
@@ -2137 +2135 @@
       }
       BondFragments = (MoleculeListClass **) Malloc(sizeof(MoleculeListClass *)*FragmentCounter, "molecule::FragmentMolecule - **BondFragments");
+      
+      // create RootStack for each Subgraph 
+      // NOTE: (keep this extern of following while loop, as lateron we may here look for which site to add to which subgraph)
+      KeyStack RootStack[FragmentCounter];
+
+      FragmentCounter = 0;
+      MolecularWalker = Subgraphs;
+      // count subgraphs and allocate fragments
+      while (MolecularWalker->next != NULL) {
+        MolecularWalker = MolecularWalker->next;
+        RootStack[FragmentCounter].clear();  
+        // find first root candidates  
+        Walker = MolecularWalker->Leaf->start;
+        while (Walker->next != MolecularWalker->Leaf->end) { // go through all (non-hydrogen) atoms
+          Walker = Walker->next;
+      #ifdef ADDHYDROGEN
+          if (Walker->type->Z != 1) // skip hydrogen
+      #endif
+            if (Walker->GetTrueFather()->AdaptiveOrder < Order) // only if Order is still greater
+              RootStack[FragmentCounter].push_front(Walker->nr);
+        }
+        FragmentCounter++;
+      }
+      
       // fill the bond fragment list
       FragmentCounter = 0;
+      TotalFragmentCounter = 0;
       MolecularWalker = Subgraphs;
       while (MolecularWalker->next != NULL) {
         MolecularWalker = MolecularWalker->next;
-        cout << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
+        *out << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
         if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
             // output ListOfBondsPerAtom for debugging
@@ -2165 +2188 @@
           *out << Verbose(0) << "Begin of bond fragmentation." << endl;
           BondFragments[FragmentCounter] = NULL;
-          if (Scheme == ANOVA) {
-            Graph *FragmentList = MolecularWalker->Leaf->FragmentBOSSANOVA(out,BottomUpOrder,configuration);
-
-            // allocate memory for the pointer array and transmorph graphs into full molecular fragments
-            int TotalNumberOfMolecules = 0;
-            for(Graph::iterator runner = FragmentList->begin(); runner != FragmentList->end(); runner++)
-              TotalNumberOfMolecules++;
-            BondFragments[FragmentCounter] = new MoleculeListClass(TotalNumberOfMolecules, AtomCount);
-            int k=0;
-            for(Graph::iterator runner = FragmentList->begin(); runner != FragmentList->end(); runner++) {
-              KeySet test = (*runner).first;
-              BondFragments[FragmentCounter]->ListOfMolecules[k] = StoreFragmentFromKeySet(out, test, configuration);
-              BondFragments[FragmentCounter]->TEList[k] = ((*runner).second).second;
-              k++;
-            }
-          }  
-          if ((Scheme == BottomUp) || (Scheme == Combined)) { // get overlapping subgraphs
-            BondFragments[FragmentCounter] = FragmentList = MolecularWalker->Leaf->FragmentBottomUp(out, BottomUpOrder, configuration, CutCyclic);
+          // call BOSSANOVA method
+          Graph *FragmentList = MolecularWalker->Leaf->FragmentBOSSANOVA(out, RootStack[FragmentCounter]);
+
+          // allocate memory for the pointer array and transmorph graphs into full molecular fragments
+          int TotalNumberOfMolecules = 0;
+          for(Graph::iterator runner = FragmentList->begin(); runner != FragmentList->end(); runner++)
+            TotalNumberOfMolecules++;
+          BondFragments[FragmentCounter] = new MoleculeListClass(TotalNumberOfMolecules, AtomCount);
+          int k=0;
+          for(Graph::iterator runner = FragmentList->begin(); runner != FragmentList->end(); runner++) {
+            KeySet test = (*runner).first;
+            *out << "Fragment No." << (*runner).second.first << " was created " << (int)(*runner).second.second << " time(s)." << endl;
+            BondFragments[FragmentCounter]->ListOfMolecules[k] = MolecularWalker->Leaf->StoreFragmentFromKeySet(out, test, configuration);
+            k++;
           }
-          if (Scheme == TopDown) { // initialise top level with whole molecule
-            *out << Verbose(2) << "Initial memory allocating and initialising for whole molecule." << endl;
-            FragmentList = new MoleculeListClass(1, MolecularWalker->Leaf->AtomCount);
-            FragmentList->ListOfMolecules[0] = MolecularWalker->Leaf->CopyMolecule();
-            FragmentList->TEList[0] = 1.;
-          }
-          if ((Scheme == Combined) || (Scheme == TopDown)) {
-            *out << Verbose(1) << "Calling TopDown." << endl;
-            BondFragments[FragmentCounter] = FragmentList->FragmentTopDown(out, TopDownOrder, BondDistance, configuration, CutCyclic);
-            // remove this molecule from list again and free wrapper list
-            delete(FragmentList);
-            FragmentList = NULL;
-          }
+          *out << k << "/" << BondFragments[FragmentCounter]->NumberOfMolecules << " fragments generated from the keysets." << endl;
         } else {
-          cout << Verbose(0) << "Connection matrix has not yet been generated!" << endl;
+          *out << Verbose(0) << "Connection matrix has not yet been generated!" << endl;
         }
         TotalFragmentCounter += BondFragments[FragmentCounter]->NumberOfMolecules;
@@ -2212 +2219 @@
         FragmentList->ListOfMolecules[TotalFragmentCounter] =  BondFragments[i]->ListOfMolecules[j];
         BondFragments[i]->ListOfMolecules[j] = NULL;
-        FragmentList->TEList[TotalFragmentCounter++] = BondFragments[i]->TEList[j];
+        TotalFragmentCounter++;
       }
       delete(BondFragments[i]);
@@ -2218 +2225 @@
     Free((void **)&BondFragments, "molecule::FragmentMolecule - **BondFragments");
   } else
-    cout << Verbose(0) << "Using fragments reconstructed from the KeySetFile." << endl;
+    *out << Verbose(0) << "Nothing to do, using only fragments reconstructed from the KeySetFile." << endl;
   // ==================================== End of FRAGMENTATION ================================
   
@@ -2241 +2248 @@
     }
     *out << Verbose(1) << "Writing " << FragmentList->NumberOfMolecules << " possible bond fragmentation configs" << endl;
-    if (FragmentList->OutputConfigForListOfFragments("BondFragment", configuration, SortIndex))
+    if (FragmentList->OutputConfigForListOfFragments(out, configuration, SortIndex))
       *out << Verbose(1) << "All configs written." << endl;
     else
       *out << Verbose(1) << "Some configs' writing failed." << endl;
     Free((void **)&SortIndex, "molecule::FragmentMolecule: *SortIndex"); 
+    
+    // === store Adjacency file ===
+    StoreAdjacencyToFile(out, configuration->configpath);
+
+    // Store adaptive orders into file
+    StoreOrderAtSiteFile(out, configuration->configpath);
     
     // restore orbital and Stop values
@@ -2256 +2269 @@
   } else
     *out << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl;
+  
   // free subgraph memory again
   if (Subgraphs != NULL) {
@@ -2266 +2280 @@
 
   *out << Verbose(0) << "End of bond fragmentation." << endl;
+};
+
+/** Stores pairs (Atom::nr, Atom::AdaptiveOrder) into file.
+ * Atoms not present in the file get "-1".
+ * \param *out output stream for debugging
+ * \param *path path to file ORDERATSITEFILE
+ * \return true - file writable, false - not writable
+ */
+bool molecule::StoreOrderAtSiteFile(ofstream *out, char *path)
+{
+  stringstream line;
+  ofstream file;
+
+  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
+  file.open(line.str().c_str());
+  *out << Verbose(0) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl;
+  if (file != NULL) {
+    atom *Walker = start;
+    while (Walker->next != end) {
+      Walker = Walker->next;
+      file << Walker->nr << "\t" << (int)Walker->AdaptiveOrder << endl;
+      *out << Verbose(2) << "Storing: " << Walker->nr << "\t" << (int)Walker->AdaptiveOrder << "." << endl;
+    }
+    file.close();
+    return true;
+  } else {
+    return false;
+  }
+};
+
+/** Parses pairs(Atom::nr, Atom::AdaptiveOrder) from file and stores in molecule's Atom's.
+ * Atoms not present in the file get "0".
+ * \param *out output stream for debugging
+ * \param *path path to file ORDERATSITEFILEe
+ * \return true - file found and scanned, false - file not found
+ * \sa ParseKeySetFile() and CheckAdjacencyFileAgainstMolecule() as this is meant to be used in conjunction with the two
+ */
+bool molecule::ParseOrderAtSiteFromFile(ofstream *out, char *path)
+{
+  unsigned char *OrderArray = (unsigned char *) Malloc(sizeof(unsigned char)*AtomCount, "molecule::ParseOrderAtSiteFromFile - *OrderArray");
+  bool status;
+  int AtomNr;
+  stringstream line;
+  ifstream file;
+  int Order;
+
+  *out << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl;
+  for(int i=0;i<AtomCount;i++)
+    OrderArray[i] = 0;
+  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
+  file.open(line.str().c_str());
+  if (file != NULL) {
+    for (int i=0;i<AtomCount;i++) // initialise with 0
+      OrderArray[i] = 0;
+    while (!file.eof()) { // parse from file
+      file >> AtomNr;
+      file >> Order;
+      OrderArray[AtomNr] = (unsigned char) Order;
+      //*out << Verbose(2) << "AtomNr " << AtomNr << " with order " << (int)OrderArray[AtomNr] << "." << endl;
+    }
+    atom *Walker = start;
+    while (Walker->next != end) { // fill into atom classes
+      Walker = Walker->next;
+      Walker->AdaptiveOrder = OrderArray[Walker->nr];
+      *out << Verbose(2) << *Walker << " gets order " << (int)Walker->AdaptiveOrder << "." << endl; 
+    }
+    file.close();
+    status = true;
+  } else {
+    status = false;
+  }
+  Free((void **)&OrderArray, "molecule::ParseOrderAtSiteFromFile - *OrderArray");
+  
+  *out << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl;
+  return status;
 };
 
@@ -2333 +2422 @@
 };
 
-/** Splits up a molecule into atomic, non-hydrogen, hydrogen-saturated fragments.
- * \param *out output stream for debugging
- * \param NumberOfTopAtoms number to initialise second parameter of MoleculeListClass with
- * \param IsAngstroem whether atomic coordination is in Angstroem (true) or atomic length/bohrradous (false)
- * \param factor additional factor TE and forces factors are multiplied with
- * \param CutCyclic whether to add cut cyclic bond or to saturate
- * \return MoleculelistClass of pointer to each atomic fragment.
- */
-MoleculeListClass * molecule::GetAtomicFragments(ofstream *out, int NumberOfTopAtoms, bool IsAngstroem, double factor, enum CutCyclicBond CutCyclic)
-{
-  atom *TopAtom = NULL, *BottomAtom = NULL; // Top = this, Bottom = AtomicFragment->ListOfMolecules[No]
-  atom *Walker = NULL;
-  MoleculeListClass *AtomicFragments = NULL;
-  atom **AtomList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::GetAtomicFragments: **AtomList");
-  for (int i=0;i<AtomCount;i++)
-    AtomList[i] = NULL;
-  bond **BondList = (bond **) Malloc(sizeof(bond *)*BondCount, "molecule::GetAtomicFragments: **AtomList");
-  for (int i=0;i<BondCount;i++)
-    BondList[i] = NULL;
-  int No = 0, Cyclic;
-
-  *out << Verbose(0) << "Begin of GetAtomicFragments." << endl;
-
-  *out << Verbose(1) << "Atoms in Molecule: ";
-  Walker = start;
-  while (Walker->next != end) {
-    Walker = Walker->next;
-    *out << Walker << "\t";
-  } 
-  *out << endl;
-#ifdef ADDHYDROGEN
-  if (NoNonHydrogen != 0) {
-    AtomicFragments = new MoleculeListClass(NoNonHydrogen, NumberOfTopAtoms);
-  } else {
-    *out << Verbose(1) << "NoNonHydrogen is " << NoNonHydrogen << ", can't allocated MoleculeListClass." << endl;
-#else
-  if (AtomCount != 0) {
-    AtomicFragments = new MoleculeListClass(AtomCount, NumberOfTopAtoms);
-  } else {
-    *out << Verbose(1) << "AtomCount is " << AtomCount << ", can't allocated MoleculeListClass." << endl;
-#endif
-    return (AtomicFragments);
-  }
-  
-  TopAtom = start;
-  while (TopAtom->next != end) {
-    TopAtom = TopAtom->next;
-  //for(int i=0;i<AtomCount;i++) {
-#ifdef ADDHYDROGEN
-    if (TopAtom->type->Z != 1) {   // regard only non-hydrogen
-#endif
-      //TopAtom = AtomsInMolecule[i];
-      *out << Verbose(1) << "Current non-Hydrogen Atom: " << TopAtom->Name << endl;
-
-      // go through all bonds to check if cyclic
-      Cyclic = 0;
-      for(int i=0;i<NumberOfBondsPerAtom[TopAtom->nr];i++)
-        Cyclic += (ListOfBondsPerAtom[TopAtom->nr][i]->Cyclic) ? 1 : 0;
-
-#ifdef ADDHYDROGEN
-      if (No > NoNonHydrogen) {
-#else
-      if (No > AtomCount) {
-#endif
-        *out << Verbose(1) << "Access on created AtomicFragmentsListOfMolecules[" << No << "] beyond NumberOfMolecules " << AtomicFragments->NumberOfMolecules << "." << endl;
-        break;
-      }
-      if (AtomList[TopAtom->nr] == NULL) {
-        // create new molecule
-        AtomicFragments->ListOfMolecules[No] = new molecule(elemente); // allocate memory
-        AtomicFragments->TEList[No] = factor;
-        AtomicFragments->ListOfMolecules[No]->BondDistance = BondDistance;
-        
-        // add central atom
-        BottomAtom = AtomicFragments->ListOfMolecules[No]->AddCopyAtom(TopAtom); // add this central atom to molecule
-        AtomList[TopAtom->nr] = BottomAtom; // mark down in list
-
-        // create fragment          
-        *out << Verbose(1) << "New fragment around atom: " << TopAtom->Name << endl;
-        BreadthFirstSearchAdd(out,AtomicFragments->ListOfMolecules[No], AtomList, BondList, TopAtom, NULL, 0, IsAngstroem, (Cyclic == 0) ? SaturateBond : CutCyclic);
-        AtomicFragments->ListOfMolecules[No]->CountAtoms(out);
-        // actually we now have to reset both arrays to NULL again, but BFS is overkill anyway for getting the atomic fragments
-        // thus we do it in O(1) and avoid the O(n) which would make this routine O(N^2)!  
-        AtomList[TopAtom->nr] = NULL;  // remove this fragment's central atom again from the list
-        
-        *out << Verbose(1) << "Atoms in Fragment " << TopAtom->nr << ": ";
-        Walker = AtomicFragments->ListOfMolecules[No]->start;
-        while (Walker->next != AtomicFragments->ListOfMolecules[No]->end) {
-          Walker = Walker->next; 
-        //for(int k=0;k<AtomicFragments->ListOfMolecules[No]->AtomCount;k++)
-          *out << Walker << "(" << Walker->father << ")\t";
-        }
-        *out << endl;
-        No++;
-      }
-#ifdef ADDHYDROGEN
-    } else
-      *out << Verbose(1) << "Current Hydrogen Atom: " << TopAtom->Name << endl;
-#endif
-  }
-
-  // output of full list before reduction
-  if (AtomicFragments != NULL) {
-    *out << "AtomicFragments: ";
-    AtomicFragments->Output(out);
-    *out << endl;
-  } else 
-    *out << Verbose(1) << "AtomicFragments is zero on return, splitting failed." << endl;
-
-  // Reducing the atomic fragments
-  if (AtomicFragments != NULL) {
-    // check whether there are equal fragments by GetMappingToUniqueFragments
-    AtomicFragments->ReduceToUniqueList(out, &cell_size[0], BondDistance);
-  } else
-    *out << Verbose(1) << "AtomicFragments is zero, reducing failed." << endl;
-  Free((void **)&BondList, "molecule::GetAtomicFragments: **BondList");
-  Free((void **)&AtomList, "molecule::GetAtomicFragments: **AtomList");
-  *out << Verbose(0) << "End of GetAtomicFragments." << endl;
-  return (AtomicFragments);
-};
-
-/** Splits up the bond in a molecule into a left and a right fragment.
- * \param *out output stream for debugging
- * \param *Bond bond to broken up into getting allocated ...
- * \param *LeftFragment ... left fragment molecule ... (ptr to the memory cell wherein the adress for the Fragment is to be stored)
- * \param *RightFragment ... and right fragment molecule to be returned.(ptr to the memory cell wherein the adress for the Fragment is to be stored)
- * \param IsAngstroem whether atomic coordination is in Angstroem (true) or atomic length/bohrradous (false)
- * \param CutCyclic whether to add cut cyclic bond or not
- * \sa FragmentTopDown()
- */
-void molecule::FragmentMoleculeByBond(ofstream *out, bond *Bond, molecule **LeftFragment, molecule **RightFragment, bool IsAngstroem, enum CutCyclicBond CutCyclic)
-{
-  *out << Verbose(0) << "Begin of FragmentMoleculeByBond." << endl; 
-#ifdef ADDHYDROGEN
-  if ((Bond->leftatom->type->Z != 1) && (Bond->rightatom->type->Z != 1)) { // if both bond partners aren't hydrogen ...
-#endif    
-    *out << Verbose(1) << "Current Non-Hydrogen Bond: " << Bond->leftatom->Name << " and " << Bond->rightatom->Name << endl;
-    *LeftFragment = new molecule(elemente);
-    *RightFragment = new molecule(elemente);
-    // initialise marker list for all atoms
-    atom **AddedAtomListLeft = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::FragmentMoleculeByBond: **AddedAtomListLeft");
-    atom **AddedAtomListRight = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::FragmentMoleculeByBond: **AddedAtomListRight");
-    for (int i=0;i<AtomCount;i++) {
-      AddedAtomListLeft[i] = NULL;
-      AddedAtomListRight[i] = NULL;
-    }
-    bond **AddedBondListLeft = (bond **) Malloc(sizeof(bond *)*BondCount, "molecule::FragmentMoleculeByBond: **AddedBondListLeft");
-    bond **AddedBondListRight = (bond **) Malloc(sizeof(bond *)*BondCount, "molecule::FragmentMoleculeByBond: **AddedBondListRight");
-    for (int i=0;i<BondCount;i++) {
-      AddedBondListLeft[i] = NULL;
-      AddedBondListRight[i] = NULL;
-    }
-  
-    // tag and add all atoms that have to be included
-    *out << Verbose(1) << "Adding BFS-wise on left hand side with Bond Order " << NoNonBonds-1 << "." << endl;
-    AddedAtomListLeft[Bond->leftatom->nr] = (*LeftFragment)->AddCopyAtom(Bond->leftatom);
-    BreadthFirstSearchAdd(out, *LeftFragment, AddedAtomListLeft, AddedBondListLeft, Bond->leftatom, Bond, 
-#ifdef ADDHYDROGEN
-    NoNonBonds
-#else
-    BondCount
-#endif    
-                                                                                                            , IsAngstroem, CutCyclic);
-    *out << Verbose(1) << "Adding BFS-wise on right hand side with Bond Order " << NoNonBonds-1 << "." << endl;
-    AddedAtomListRight[Bond->rightatom->nr] = (*RightFragment)->AddCopyAtom(Bond->rightatom);
-    BreadthFirstSearchAdd(out, *RightFragment, AddedAtomListRight, AddedBondListRight, Bond->rightatom, Bond, 
-#ifdef ADDHYDROGEN
-    NoNonBonds
-#else
-    BondCount
-#endif    
-                                                                                                            , IsAngstroem, CutCyclic);  
- 
-    // count atoms
-    (*LeftFragment)->CountAtoms(out);
-    (*RightFragment)->CountAtoms(out);
-    // free all and exit
-    Free((void **)&AddedAtomListLeft, "molecule::FragmentMoleculeByBond: **AddedAtomListLeft");
-    Free((void **)&AddedAtomListRight, "molecule::FragmentMoleculeByBond: **AddedAtomListRight");
-    Free((void **)&AddedBondListLeft, "molecule::FragmentMoleculeByBond: **AddedBondListLeft");
-    Free((void **)&AddedBondListRight, "molecule::FragmentMoleculeByBond: **AddedBondListRight");
-#ifdef ADDHYDROGEN
-  }
-#endif
-  *out << Verbose(0) << "End of FragmentMoleculeByBond." << endl;
-};
-
-/** Returns the given \a **FragmentList filled with molecules around each bond including up to \a BondDegree neighbours.
- * \param *out output stream for debugging
- * \param BondOrder neighbours on each side to be ...
- * \param IsAngstroem whether atomic coordination is in Angstroem (true) or atomic length/bohrradous (false)
- * \param CutCyclic whether to add cut cyclic bond or to saturate
- * \sa FragmentBottomUp(), molecule::AddBondOrdertoMolecule()
- */
-MoleculeListClass * molecule::GetEachBondFragmentOfOrder(ofstream *out, int BondOrder, bool IsAngstroem, enum CutCyclicBond CutCyclic)
-{
-  /// Allocate memory for Bond list and go through each bond and fragment molecule up to bond order and fill the list to be returned.
-  MoleculeListClass *FragmentList = NULL;
-  atom **AddedAtomList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::GetBondFragmentOfOrder: **AddedAtomList");
-  bond **AddedBondList = (bond **) Malloc(sizeof(bond *)*BondCount, "molecule::GetBondFragmentOfOrder: **AddedBondList");
-  bond *Binder = NULL;
-
-  *out << Verbose(0) << "Begin of GetEachBondFragmentOfOrder." << endl;
-#ifdef ADDHYDROGEN
-  if (NoNonBonds != 0) {
-    FragmentList = new MoleculeListClass(NoNonBonds, AtomCount);
-  } else {
-    *out << Verbose(1) << "NoNonBonds is " << NoNonBonds << ", can't allocate list." << endl;
-#else
-  if (BondCount != 0) {
-    FragmentList = new MoleculeListClass(BondCount, AtomCount);
-  } else {
-    *out << Verbose(1) << "BondCount is " << BondCount << ", can't allocate list." << endl;
-#endif
-  }
-  int No = 0;
-  Binder = first;
-  while (Binder->next != last) { // get each bond, NULL is returned if it is a H-H bond
-    Binder = Binder->next;
-#ifdef ADDHYDROGEN
-    if ((Binder->leftatom->type->Z != 1) && (Binder->rightatom->type->Z != 1))  // if both bond partners aren't hydrogen ...
-#endif
-      if ((CutCyclic == SaturateBond) || (!Binder->Cyclic)) {
-        *out << Verbose(1) << "Getting Fragment for Non-Hydrogen Bond: " << Binder->leftatom->Name << " and " << Binder->rightatom->Name << endl;
-        FragmentList->ListOfMolecules[No] = new molecule(elemente);
-        // initialise marker list for all atoms
-        for (int i=0;i<AtomCount;i++)
-          AddedAtomList[i] = NULL;
-        for (int i=0;i<BondCount;i++)
-          AddedBondList[i] = NULL;
-      
-        // add root bond as first bond (this is needed later on fragmenting)
-        *out << Verbose(1) << "Adding Root Bond " << *Binder << " and its atom." << endl;
-        AddedAtomList[Binder->leftatom->nr] = FragmentList->ListOfMolecules[No]->AddCopyAtom(Binder->leftatom);
-        AddedAtomList[Binder->rightatom->nr] = FragmentList->ListOfMolecules[No]->AddCopyAtom(Binder->rightatom);
-        AddedBondList[Binder->nr] = FragmentList->ListOfMolecules[No]->AddBond(AddedAtomList[Binder->leftatom->nr], AddedAtomList[Binder->rightatom->nr], Binder->BondDegree);
-    
-        // tag and add all atoms that have to be included
-        *out << Verbose(1) << "Adding BFS-wise on left hand side." << endl;
-        BreadthFirstSearchAdd(out, FragmentList->ListOfMolecules[No], AddedAtomList, AddedBondList, Binder->leftatom, NULL, BondOrder, IsAngstroem, CutCyclic);  
-        *out << Verbose(1) << "Adding BFS-wise on right hand side." << endl;
-        BreadthFirstSearchAdd(out, FragmentList->ListOfMolecules[No], AddedAtomList, AddedBondList, Binder->rightatom, NULL, BondOrder, IsAngstroem, CutCyclic);  
-        
-        // count atoms
-        FragmentList->ListOfMolecules[No]->CountAtoms(out);
-        FragmentList->TEList[No] = 1.;
-        *out << Verbose(1) << "GetBondFragmentOfOrder: " << Binder->nr << "th Fragment: " << FragmentList->ListOfMolecules[No] << "." << endl;
-        No++;
-      }
-  }
-  // free all lists
-  Free((void **)&AddedAtomList, "molecule::GetBondFragmentOfOrder: **AddedAtomList");
-  Free((void **)&AddedBondList, "molecule::GetBondFragmentOfOrder: **AddedBondList");
-  // output and exit
-  FragmentList->Output(out);
-  *out << Verbose(0) << "End of GetEachBondFragmentOfOrder." << endl;
-  return (FragmentList);
-}; 
-
 /** Adds atoms up to \a BondCount distance from \a *Root and notes them down in \a **AddedAtomList.
  * Gray vertices are always enqueued in an AtomStackClass FIFO queue, the rest is usual BFS with adding vertices found was
@@ -2603 +2433 @@
  * \param BondOrder maximum distance for vertices to add
  * \param IsAngstroem lengths are in angstroem or bohrradii
- * \param CutCyclic whether to cut cyclic bonds (means saturate on need with hydrogen) or to always add
  */  
-void molecule::BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem, enum CutCyclicBond CutCyclic)
+void molecule::BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem)
 {
   atom **PredecessorList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::BreadthFirstSearchAdd: **PredecessorList");
@@ -2650 +2479 @@
           ShortestPathList[OtherAtom->nr] = ShortestPathList[Walker->nr]+1;
           *out << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " " << ((ColorList[OtherAtom->nr] == white) ? "white" : "lightgray") << ", its predecessor is " << Walker->Name << " and its Shortest Path is " << ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl; 
-          if ((((ShortestPathList[OtherAtom->nr] < BondOrder) && (Binder != Bond)) || (Binder->Cyclic && (CutCyclic == KeepBond))) ) { // Check for maximum distance
+          if ((((ShortestPathList[OtherAtom->nr] < BondOrder) && (Binder != Bond))) ) { // Check for maximum distance
             *out << Verbose(3);
             if (AddedAtomList[OtherAtom->nr] == NULL) { // add if it's not been so far
@@ -2678 +2507 @@
             else if (ShortestPathList[OtherAtom->nr] >= BondOrder)
               *out << Verbose(3) << "Not Queueing, is out of Bond Count of " << BondOrder;
-            if ((Binder->Cyclic && (CutCyclic != KeepBond)))
-              *out << ", is part of a cyclic bond yet we don't keep them, saturating bond with Hydrogen." << endl;
             if (!Binder->Cyclic)
               *out << ", is not part of a cyclic bond, saturating bond with Hydrogen." << endl;
             if (AddedBondList[Binder->nr] == NULL) {
-              if ((AddedAtomList[OtherAtom->nr] != NULL) && (CutCyclic == KeepBond)) { // .. whether we add or saturate
+              if ((AddedAtomList[OtherAtom->nr] != NULL)) { // .. whether we add or saturate
                 AddedBondList[Binder->nr] = Mol->AddBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder->BondDegree);
                 AddedBondList[Binder->nr]->Cyclic = Binder->Cyclic;
@@ -2698 +2525 @@
           // This has to be a cyclic bond, check whether it's present ...
           if (AddedBondList[Binder->nr] == NULL) {
-            if ((Binder != Bond) && (Binder->Cyclic) && (((ShortestPathList[Walker->nr]+1) < BondOrder) || (CutCyclic == KeepBond))) { 
+            if ((Binder != Bond) && (Binder->Cyclic) && (((ShortestPathList[Walker->nr]+1) < BondOrder))) { 
               AddedBondList[Binder->nr] = Mol->AddBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder->BondDegree);
               AddedBondList[Binder->nr]->Cyclic = Binder->Cyclic;
@@ -3106 +2933 @@
   bool **UsedList;
   bond **BondsPerSPList;
-  double TEFactor;
   int *BondsPerSPCount;
 };
@@ -3165 +2991 @@
           *out << Verbose(2+verbosity) << "Adding " << *OtherWalker << " with nr " << OtherWalker->nr << "." << endl;
           TouchedList[TouchedIndex++] = OtherWalker->nr;  // note as added
-          FragmentSearch->FragmentSet->insert(OtherWalker->GetTrueFather()->nr);
+          FragmentSearch->FragmentSet->insert(OtherWalker->nr);
             //FragmentSearch->UsedList[OtherWalker->nr][i] = true;
           //}
@@ -3205 +3031 @@
         *out << Verbose(1+verbosity) << "Enough items on stack for a fragment!" << endl;
         // store fragment as a KeySet
-        *out << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], indices are: ";
-        for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++) {
-          *out << (*runner)+1 << " "; 
-        }
+        *out << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], local nr.s are: ";
+        for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++)
+          *out << (*runner) << " "; 
         InsertFragmentIntoGraph(out, FragmentSearch);
-        Removal = LookForRemovalCandidate(out, FragmentSearch->FragmentSet, FragmentSearch->ShortestPathList);
+        //Removal = LookForRemovalCandidate(out, FragmentSearch->FragmentSet, FragmentSearch->ShortestPathList);
         //Removal = StoreFragmentFromStack(out, FragmentSearch->Root, FragmentSearch->Leaflet, FragmentSearch->FragmentStack, FragmentSearch->ShortestPathList,FragmentSearch->Labels, &FragmentSearch->FragmentCounter, FragmentSearch->configuration);
       }
@@ -3218 +3043 @@
       for(int j=0;j<TouchedIndex;j++) {
         Removal = TouchedList[j];
-        *out << Verbose(2+verbosity) << "Removing item nr. " << Removal+1 << " from snake stack." << endl;
+        *out << Verbose(2+verbosity) << "Removing item nr. " << Removal << " from snake stack." << endl;
         FragmentSearch->FragmentSet->erase(Removal);
         TouchedList[j] = -1;
       }
+      *out << Verbose(2) << "Remaining local nr.s on snake stack are: ";
+      for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++)
+        *out << (*runner) << " "; 
+      *out << endl;
       TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
     } else {
@@ -3228 +3057 @@
   }
   Free((void **)&TouchedList, "molecule::SPFragmentGenerator: *TouchedList");  
-  *out << Verbose(1+verbosity) << "End of SPFragmentGenerator " << RootDistance << " away from Root " << *FragmentSearch->Root << " and SubOrder is " << SubOrder << "." << endl;
-};
-
-/** Creates a list of all unique fragments of certain vertex size from a given graph \a Fragment in the context of \a this molecule.
+  *out << Verbose(1+verbosity) << "End of SPFragmentGenerator, " << RootDistance << " away from Root " << *FragmentSearch->Root << " and SubOrder is " << SubOrder << "." << endl;
+};
+
+/** Creates a list of all unique fragments of certain vertex size from a given graph \a Fragment for a given root vertex in the context of \a this molecule.
  * Note that we may use the fact that the atoms are SP-ordered on the atomstack. I.e. when popping always the last, we first get all
  * with SP of 2, then those with SP of 3, then those with SP of 4 and so on.
  * \param *out output stream for debugging
- * \param Order number of vertices
- * \param *ListOfGraph Graph structure to insert found fragments into
- * \param Fragment Restricted vertex set to use in context of molecule
- * \param TEFactor TEFactor to store in graphlist in the end
- * \param *configuration configuration needed for IsAngstroem
+ * \param Order bond order (limits BFS exploration and "number of digits" in power set generation 
+ * \param *ReturnKeySets Graph structure to insert found keysets/fragments into
+ * \param RestrictedKeySet Restricted vertex set to use in context of molecule
+ * \param RootKeyNr Atom::nr of the atom acting as current fragment root 
  * \return number of inserted fragments
  * \note ShortestPathList in FragmentSearch structure is probably due to NumberOfAtomsSPLevel and SP not needed anymore
  */
-int molecule::CreateListOfUniqueFragmentsOfOrder(ofstream *out, int Order, Graph *ListOfGraph, KeySet Fragment, double TEFactor, config *configuration) 
-{
-  int SP, UniqueIndex, RootKeyNr, AtomKeyNr;
-  int *NumberOfAtomsSPLevel = (int *) Malloc(sizeof(int)*Order, "molecule::CreateListOfUniqueFragmentsOfOrder: *SPLevelCount");
+int molecule::PowerSetGenerator(ofstream *out, int Order, Graph *ReturnKeySets, KeySet RestrictedKeySet, int RootKeyNr) 
+{
+  int SP, UniqueIndex, AtomKeyNr;
+  int *NumberOfAtomsSPLevel = (int *) Malloc(sizeof(int)*Order, "molecule::PowerSetGenerator: *SPLevelCount");
   atom *Walker = NULL, *OtherWalker = NULL;
   bond *Binder = NULL;
   bond **BondsList = NULL;
-  KeyStack RootStack;
   KeyStack AtomStack;
-  atom **PredecessorList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: **PredecessorList");
+  atom **PredecessorList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::PowerSetGenerator: **PredecessorList");
   KeySet::iterator runner;
+  //int Count = RestrictedKeySet.size();
 
   // initialise the fragments structure
   struct UniqueFragments FragmentSearch;
-  FragmentSearch.BondsPerSPList = (bond **) Malloc(sizeof(bond *)*Order*2, "molecule::CreateListOfUniqueFragmentsOfOrder: ***BondsPerSPList");
-  FragmentSearch.BondsPerSPCount = (int *) Malloc(sizeof(int)*Order, "molecule::CreateListOfUniqueFragmentsOfOrder: *BondsPerSPCount");
-  FragmentSearch.ShortestPathList = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *ShortestPathList");
-  FragmentSearch.Labels = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *Labels");
+  FragmentSearch.BondsPerSPList = (bond **) Malloc(sizeof(bond *)*Order*2, "molecule::PowerSetGenerator: ***BondsPerSPList");
+  FragmentSearch.BondsPerSPCount = (int *) Malloc(sizeof(int)*Order, "molecule::PowerSetGenerator: *BondsPerSPCount");
+  FragmentSearch.ShortestPathList = (int *) Malloc(sizeof(int)*AtomCount, "molecule::PowerSetGenerator: *ShortestPathList");
+  FragmentSearch.Labels = (int *) Malloc(sizeof(int)*AtomCount, "molecule::PowerSetGenerator: *Labels");
   FragmentSearch.FragmentCounter = 0;
   FragmentSearch.FragmentSet = new KeySet;
-  FragmentSearch.configuration = configuration;
-  FragmentSearch.TEFactor = TEFactor;
-  FragmentSearch.Leaflet = ListOfGraph;      // set to insertion graph
+  FragmentSearch.Leaflet = ReturnKeySets;      // set to insertion graph
+  FragmentSearch.Root = FindAtom(RootKeyNr);
   for (int i=0;i<AtomCount;i++) {
     FragmentSearch.Labels[i] = -1;
@@ -3280 +3107 @@
   
   *out << endl;
-  *out << Verbose(0) << "Begin of CreateListOfUniqueFragmentsOfOrder with order " << Order << "." << endl;
-
-  RootStack.clear();  
-  // find first root candidates  
-  runner = Fragment.begin();
-  Walker = NULL;
-  while ((Walker == NULL) && (runner != Fragment.end())) { // search for first non-hydrogen atom
-    Walker = FindAtom((*runner));
-    *out << Verbose(4) << "Current Root candidate is " << Walker->Name << "." << endl;
+  *out << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl;
+
+  UniqueIndex = 0;
+  if (FragmentSearch.Labels[RootKeyNr] == -1)
+    FragmentSearch.Labels[RootKeyNr] = UniqueIndex++;
+  FragmentSearch.ShortestPathList[RootKeyNr] = 0;
+  // prepare the atom stack counters (number of atoms with certain SP on stack)
+  for (int i=0;i<Order;i++)
+    NumberOfAtomsSPLevel[i] = 0;
+  NumberOfAtomsSPLevel[0] = 1;  // for root
+  SP = -1;
+  *out << endl;
+  *out << Verbose(0) << "Starting BFS analysis ..." << endl;
+  // push as first on atom stack and goooo ...
+  AtomStack.clear();  
+  AtomStack.push_back(RootKeyNr);
+  *out << Verbose(0) << "Cleared AtomStack and pushed root as first item onto it." << endl;
+  // do a BFS search to fill the SP lists and label the found vertices
+  while (!AtomStack.empty()) {
+    // pop next atom
+    AtomKeyNr = AtomStack.front();
+    AtomStack.pop_front();
+    if (SP != -1)
+      NumberOfAtomsSPLevel[SP]--;
+    if ((SP == -1) || (NumberOfAtomsSPLevel[SP] == -1)) {
+      SP++;
+      NumberOfAtomsSPLevel[SP]--; // carry over "-1" to next level
+      *out << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with 0 item(s)";
+      if (SP > 0)
+        *out << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl;
+      else
+        *out << "." << endl;
+      FragmentSearch.BondsPerSPCount[SP] = 0;
+    } else {
+      *out << Verbose(1) << "Still " << NumberOfAtomsSPLevel[SP]+1 << " on this SP (" << SP << ") level, currently having " << FragmentSearch.BondsPerSPCount[SP] << " item(s)." << endl;
+    }
+    Walker = FindAtom(AtomKeyNr);
+    *out << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and label " << FragmentSearch.Labels[AtomKeyNr] << " and SP of " << SP << "." << endl;
+    // check for new sp level
+    // go through all its bonds
+    *out << Verbose(1) << "Going through all bonds of Walker." << endl;
+    for (int i=0;i<NumberOfBondsPerAtom[AtomKeyNr];i++) {
+      Binder = ListOfBondsPerAtom[AtomKeyNr][i];
+      OtherWalker = Binder->GetOtherAtom(Walker);
+      if ((RestrictedKeySet.find(OtherWalker->nr) != RestrictedKeySet.end())
 #ifdef ADDHYDROGEN
-    if (Walker->type->Z == 1) // skip hydrogen
-      Walker = NULL;
+       && (OtherWalker->type->Z != 1)
 #endif
-    runner++;
-  }
-  if (Walker != NULL)
-    RootStack.push_back(Walker->nr);
-  else
-    *out << Verbose(0) << "ERROR: Could not find an appropriate Root atom!" << endl;
-  
-  UniqueIndex = 0;
-  while (!RootStack.empty()) {
-    // Get Root and prepare
-    RootKeyNr = RootStack.front();
-    RootStack.pop_front();
-    FragmentSearch.Root = FindAtom(RootKeyNr);
-    if (FragmentSearch.Labels[RootKeyNr] == -1)
-      FragmentSearch.Labels[RootKeyNr] = UniqueIndex++;
-    FragmentSearch.ShortestPathList[RootKeyNr] = 0;
-    // prepare the atom stack counters (number of atoms with certain SP on stack)
-    for (int i=0;i<Order;i++)
-      NumberOfAtomsSPLevel[i] = 0;
-    NumberOfAtomsSPLevel[0] = 1;  // for root
-    SP = -1;
-    *out << endl;
-    *out << Verbose(0) << "Starting BFS analysis with current Root: " << *FragmentSearch.Root << "." << endl;
-    // push as first on atom stack and goooo ...
-    AtomStack.clear();  
-    AtomStack.push_back(RootKeyNr);
-    *out << Verbose(0) << "Cleared AtomStack and pushed root as first item onto it." << endl;
-    // do a BFS search to fill the SP lists and label the found vertices
-    while (!AtomStack.empty()) {
-      // pop next atom
-      AtomKeyNr = AtomStack.front();
-      AtomStack.pop_front();
-      if (SP != -1)
-        NumberOfAtomsSPLevel[SP]--;
-      if ((SP == -1) || (NumberOfAtomsSPLevel[SP] == -1)) {
-      ////if (SP < FragmentSearch.ShortestPathList[AtomKeyNr]) { // bfs has reached new SP level, hence allocate for new list
-        SP++;
-        NumberOfAtomsSPLevel[SP]--; // carry over "-1" to next level
-        ////SP = FragmentSearch.ShortestPathList[AtomKeyNr];
-        *out << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with 0 item(s)";
-        if (SP > 0)
-          *out << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl;
-        else
-          *out << "." << endl;
-        FragmentSearch.BondsPerSPCount[SP] = 0;
-      } else {
-        *out << Verbose(1) << "Still " << NumberOfAtomsSPLevel[SP]+1 << " on this SP (" << SP << ") level, currently having " << FragmentSearch.BondsPerSPCount[SP] << " item(s)." << endl;
-      }
-      Walker = FindAtom(AtomKeyNr);
-      *out << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and label " << FragmentSearch.Labels[AtomKeyNr] << " and SP of " << SP << "." << endl;
-      // check for new sp level
-      // go through all its bonds
-      *out << Verbose(1) << "Going through all bonds of Walker." << endl;
-      for (int i=0;i<NumberOfBondsPerAtom[AtomKeyNr];i++) {
-        Binder = ListOfBondsPerAtom[AtomKeyNr][i];
-        OtherWalker = Binder->GetOtherAtom(Walker);
-        if ((Fragment.find(OtherWalker->nr) != Fragment.end())
-#ifdef ADDHYDROGEN
-         && (OtherWalker->type->Z != 1)
-#endif
-                                                              ) {  // skip hydrogens and restrict to fragment
-          *out << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *Binder << "." << endl;
-          // set the label if not set (and push on root stack as well)
-          if (FragmentSearch.Labels[OtherWalker->nr] == -1) {
-            RootStack.push_back(OtherWalker->nr);
-            FragmentSearch.Labels[OtherWalker->nr] = UniqueIndex++;
-            *out << Verbose(3) << "Set label to " << FragmentSearch.Labels[OtherWalker->nr] << "." << endl;
-          } else {
-            *out << Verbose(3) << "Label is already " << FragmentSearch.Labels[OtherWalker->nr] << "." << endl;
-          }
-          if ((OtherWalker != PredecessorList[AtomKeyNr]) && (FragmentSearch.Labels[OtherWalker->nr] > FragmentSearch.Labels[RootKeyNr])) { // only pass through those with label bigger than Root's
-            // set shortest path if not set or longer
-            //if ((FragmentSearch.ShortestPathList[OtherWalker->nr] == -1) || (FragmentSearch.ShortestPathList[OtherWalker->nr] > FragmentSearch.ShortestPathList[AtomKeyNr]))  {
-              FragmentSearch.ShortestPathList[OtherWalker->nr] = SP+1;
-              *out << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl;
-            //} else {
-            //  *out << Verbose(3) << "Shortest Path is already " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl;
-            //}
-            if (FragmentSearch.ShortestPathList[OtherWalker->nr] < Order) { // only pass through those within reach of Order
-              // push for exploration on stack (only if the SP of OtherWalker is longer than of Walker! (otherwise it has been added already!)
-              if (FragmentSearch.ShortestPathList[OtherWalker->nr] > SP) {
-                if (FragmentSearch.ShortestPathList[OtherWalker->nr] < (Order-1)) {
-                  *out << Verbose(3) << "Putting on atom stack for further exploration." << endl;
-                  PredecessorList[OtherWalker->nr] = Walker;    // note down the one further up the exploration tree
-                  AtomStack.push_back(OtherWalker->nr);
-                  NumberOfAtomsSPLevel[FragmentSearch.ShortestPathList[OtherWalker->nr]]++;
-                } else {
-                  *out << Verbose(3) << "Not putting on atom stack, is at end of reach." << endl;
-                }
-                // add the bond in between to the SP list
-                Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
-                add(Binder, FragmentSearch.BondsPerSPList[2*SP+1]);
-                FragmentSearch.BondsPerSPCount[SP]++;
-                *out << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP] << " item(s)." << endl;
+                                                            ) {  // skip hydrogens and restrict to fragment
+        *out << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *Binder << "." << endl;
+        // set the label if not set (and push on root stack as well)
+        if (FragmentSearch.Labels[OtherWalker->nr] == -1) {
+          FragmentSearch.Labels[OtherWalker->nr] = UniqueIndex++;
+          *out << Verbose(3) << "Set label to " << FragmentSearch.Labels[OtherWalker->nr] << "." << endl;
+        } else {
+          *out << Verbose(3) << "Label is already " << FragmentSearch.Labels[OtherWalker->nr] << "." << endl;
+        }
+        if ((OtherWalker != PredecessorList[AtomKeyNr]) && (FragmentSearch.Labels[OtherWalker->nr] > FragmentSearch.Labels[RootKeyNr])) { // only pass through those with label bigger than Root's
+          FragmentSearch.ShortestPathList[OtherWalker->nr] = SP+1;
+          *out << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl;
+          if (FragmentSearch.ShortestPathList[OtherWalker->nr] < Order) { // only pass through those within reach of Order
+            // push for exploration on stack (only if the SP of OtherWalker is longer than of Walker! (otherwise it has been added already!)
+            if (FragmentSearch.ShortestPathList[OtherWalker->nr] > SP) {
+              if (FragmentSearch.ShortestPathList[OtherWalker->nr] < (Order-1)) {
+                *out << Verbose(3) << "Putting on atom stack for further exploration." << endl;
+                PredecessorList[OtherWalker->nr] = Walker;    // note down the one further up the exploration tree
+                AtomStack.push_back(OtherWalker->nr);
+                NumberOfAtomsSPLevel[FragmentSearch.ShortestPathList[OtherWalker->nr]]++;
               } else {
-                *out << Verbose(3) << "Not putting on atom stack, nor adding bond, as " << *OtherWalker << "'s SP is shorter than Walker's." << endl;
+                *out << Verbose(3) << "Not putting on atom stack, is at end of reach." << endl;
               }
-            } else {
-              *out << Verbose(3) << "Not continuing, as " << *OtherWalker << " is out of reach of order " << Order << "." << endl;
-            }
-          } else {
-            *out << Verbose(3) << "Not passing on, as label of " << *OtherWalker << " " << FragmentSearch.Labels[OtherWalker->nr] << " is smaller than that of Root " << FragmentSearch.Labels[RootKeyNr] << " or this is my predecessor." << endl;
-          }
-        } else {
-          *out << Verbose(2) << "Is not in the Fragment or skipping hydrogen " << *OtherWalker << "." << endl;
-        }
-      }
-    }
-    // reset predecessor list
-    for(int i=0;i<Order;i++) {
-      Binder = FragmentSearch.BondsPerSPList[2*i];
-      *out << Verbose(1) << "Current SP level is " << i << "." << endl;
-      while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
+              // add the bond in between to the SP list
+              Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
+              add(Binder, FragmentSearch.BondsPerSPList[2*SP+1]);
+              FragmentSearch.BondsPerSPCount[SP]++;
+              *out << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP] << " item(s)." << endl;
+            } else *out << Verbose(3) << "Not putting on atom stack, nor adding bond, as " << *OtherWalker << "'s SP is shorter than Walker's." << endl;
+          } else *out << Verbose(3) << "Not continuing, as " << *OtherWalker << " is out of reach of order " << Order << "." << endl;
+        } else *out << Verbose(3) << "Not passing on, as label of " << *OtherWalker << " " << FragmentSearch.Labels[OtherWalker->nr] << " is smaller than that of Root " << FragmentSearch.Labels[RootKeyNr] << " or this is my predecessor." << endl;
+      } else *out << Verbose(2) << "Is not in the retstricted keyset or skipping hydrogen " << *OtherWalker << "." << endl;
+    }
+  }
+  // reset predecessor list
+  for(int i=0;i<Order;i++) {
+    Binder = FragmentSearch.BondsPerSPList[2*i];
+    *out << Verbose(1) << "Current SP level is " << i << "." << endl;
+    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
+      Binder = Binder->next;
+      PredecessorList[Binder->rightatom->nr] = NULL;  // By construction "OtherAtom" is always Bond::rightatom!
+    } 
+  }
+  *out << endl;
+  
+  // outputting all list for debugging
+  *out << Verbose(0) << "Printing all found lists." << endl;
+  for(int i=0;i<Order;i++) {
+    Binder = FragmentSearch.BondsPerSPList[2*i];
+    *out << Verbose(1) << "Current SP level is " << i << "." << endl;
+    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
+      Binder = Binder->next;
+      *out << Verbose(2) << *Binder << endl;
+    } 
+  }
+  
+  // creating fragments with the found edge sets
+  SP = 0;
+  for(int i=0;i<Order;i++) { // sum up all found edges
+    Binder = FragmentSearch.BondsPerSPList[2*i];
+    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
+      Binder = Binder->next;
+      SP ++; 
+    }
+  }
+  *out << Verbose(0) << "Total number of edges is " << SP << "." << endl;
+  if (SP >= (Order-1)) {
+    // start with root (push on fragment stack)
+    *out << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << ", local nr is " << FragmentSearch.Root->nr << "." << endl;
+    FragmentSearch.FragmentSet->clear();  
+    FragmentSearch.FragmentSet->insert(FragmentSearch.Root->nr);
+    
+    if (FragmentSearch.FragmentSet->size() == (unsigned int) Order) {
+      *out << Verbose(0) << "Enough items on stack already for a fragment!" << endl;
+      // store fragment as a KeySet
+      *out << Verbose(2) << "Found a new fragment[" << FragmentSearch.FragmentCounter << "], local nr.s are: ";
+      for(KeySet::iterator runner = FragmentSearch.FragmentSet->begin(); runner != FragmentSearch.FragmentSet->end(); runner++) {
+        *out << (*runner) << " "; 
+      }
+      *out << endl;
+      InsertFragmentIntoGraph(out, &FragmentSearch);
+    } else {
+      *out << Verbose(0) << "Preparing subset for this root and calling generator." << endl;
+      // prepare the subset and call the generator
+      BondsList = (bond **) Malloc(sizeof(bond *)*FragmentSearch.BondsPerSPCount[0], "molecule::PowerSetGenerator: **BondsList");
+      Binder = FragmentSearch.BondsPerSPList[0];
+      for(int i=0;i<FragmentSearch.BondsPerSPCount[0];i++) {
         Binder = Binder->next;
-        PredecessorList[Binder->rightatom->nr] = NULL;  // By construction "OtherAtom" is always Bond::rightatom!
-      } 
-    }
-    *out << endl;
-    *out << Verbose(0) << "Printing all found lists." << endl;
-    // outputting all list for debugging
-    for(int i=0;i<Order;i++) {
-      Binder = FragmentSearch.BondsPerSPList[2*i];
-      *out << Verbose(1) << "Current SP level is " << i << "." << endl;
-      while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
-        Binder = Binder->next;
-        *out << Verbose(2) << *Binder << endl;
-      } 
-    }
-    
-    // creating fragments with the found edge sets
-    SP = 0;
-    for(int i=0;i<Order;i++) { // sum up all found edges
-      Binder = FragmentSearch.BondsPerSPList[2*i];
-      while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
-        Binder = Binder->next;
-        SP ++; 
-      }
-    }
-    *out << Verbose(0) << "Total number of edges is " << SP << "." << endl;
-    if (SP >= (Order-1)) {
-      // start with root (push on fragment stack)
-      *out << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << "." << endl;
-      FragmentSearch.FragmentSet->clear();  
-      FragmentSearch.FragmentSet->insert(FragmentSearch.Root->GetTrueFather()->nr);
-      
-      if (FragmentSearch.FragmentSet->size() == (unsigned int) Order) {
-        *out << Verbose(0) << "Enough items on stack already for a fragment!" << endl;
-        // store fragment as a KeySet
-        *out << Verbose(2) << "Found a new fragment[" << FragmentSearch.FragmentCounter << "], indices are: ";
-        for(KeySet::iterator runner = FragmentSearch.FragmentSet->begin(); runner != FragmentSearch.FragmentSet->end(); runner++) {
-          *out << (*runner)+1 << " "; 
-        }
-        *out << endl;
-        InsertFragmentIntoGraph(out, &FragmentSearch);
-        //StoreFragmentFromStack(out, FragmentSearch.Root, FragmentSearch.Leaflet, FragmentSearch.FragmentStack, FragmentSearch.ShortestPathList,FragmentSearch.Labels, &FragmentSearch.FragmentCounter, FragmentSearch.configuration);
-      } else {
-        *out << Verbose(0) << "Preparing subset for this root and calling generator." << endl;
-        // prepare the subset and call the generator
-        BondsList = (bond **) Malloc(sizeof(bond *)*FragmentSearch.BondsPerSPCount[0], "molecule::CreateListOfUniqueFragmentsOfOrder: **BondsList");
-        Binder = FragmentSearch.BondsPerSPList[0];
-        for(int i=0;i<FragmentSearch.BondsPerSPCount[0];i++) {
-          Binder = Binder->next;
-          BondsList[i] = Binder;
-        }
-        SPFragmentGenerator(out, &FragmentSearch, 0, BondsList, FragmentSearch.BondsPerSPCount[0], Order-1);  
-        Free((void **)&BondsList, "molecule::CreateListOfUniqueFragmentsOfOrder: **BondsList");
-      }
-    } else {
-      *out << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl;
-    }
-    
-    // remove root from stack
-    *out << Verbose(0) << "Removing root again from stack." << endl;
-    FragmentSearch.FragmentSet->erase(FragmentSearch.Root->nr);    
-
-    // free'ing the bonds lists
-    *out << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl;
-    for(int i=0;i<Order;i++) {
-      *out << Verbose(1) << "Current SP level is " << i << ": ";
-      Binder = FragmentSearch.BondsPerSPList[2*i];
-      while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
-        Binder = Binder->next;
-        FragmentSearch.ShortestPathList[Binder->leftatom->nr] = -1;
-        FragmentSearch.ShortestPathList[Binder->rightatom->nr] = -1;
-      }
-      // delete added bonds
-      cleanup(FragmentSearch.BondsPerSPList[2*i], FragmentSearch.BondsPerSPList[2*i+1]);
-      // also start and end node
-      *out << "cleaned." << endl;
-    }
-  }
-  
+        BondsList[i] = Binder;
+      }
+      SPFragmentGenerator(out, &FragmentSearch, 0, BondsList, FragmentSearch.BondsPerSPCount[0], Order-1);  
+      Free((void **)&BondsList, "molecule::PowerSetGenerator: **BondsList");
+    }
+  } else {
+    *out << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl;
+  }
+
+/*  // as FragmentSearch structure is used only once, we don't have to clean it anymore
+  // remove root from stack
+  *out << Verbose(0) << "Removing root again from stack." << endl;
+  FragmentSearch.FragmentSet->erase(FragmentSearch.Root->nr);    
+
+  // free'ing the bonds lists
+  *out << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl;
+  for(int i=0;i<Order;i++) {
+    *out << Verbose(1) << "Current SP level is " << i << ": ";
+    Binder = FragmentSearch.BondsPerSPList[2*i];
+    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
+      Binder = Binder->next;
+      // *out << "Removing atom " << Binder->leftatom->nr << " and " << Binder->rightatom->nr << "." << endl; // make sure numbers are local
+      FragmentSearch.ShortestPathList[Binder->leftatom->nr] = -1;
+      FragmentSearch.ShortestPathList[Binder->rightatom->nr] = -1;
+    }
+    // delete added bonds
+    cleanup(FragmentSearch.BondsPerSPList[2*i], FragmentSearch.BondsPerSPList[2*i+1]);
+    // also start and end node
+    *out << "cleaned." << endl;
+  }
+*/
   // free allocated memory
-  Free((void **)&NumberOfAtomsSPLevel, "molecule::CreateListOfUniqueFragmentsOfOrder: *SPLevelCount");
-  Free((void **)&PredecessorList, "molecule::CreateListOfUniqueFragmentsOfOrder: **PredecessorList");
+  Free((void **)&NumberOfAtomsSPLevel, "molecule::PowerSetGenerator: *SPLevelCount");
+  Free((void **)&PredecessorList, "molecule::PowerSetGenerator: **PredecessorList");
   for(int i=0;i<Order;i++) { // delete start and end of each list
     delete(FragmentSearch.BondsPerSPList[2*i]);
     delete(FragmentSearch.BondsPerSPList[2*i+1]);
   }
-  Free((void **)&FragmentSearch.BondsPerSPList, "molecule::CreateListOfUniqueFragmentsOfOrder: ***BondsPerSPList");
-  Free((void **)&FragmentSearch.BondsPerSPCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *BondsPerSPCount");
-  Free((void **)&FragmentSearch.ShortestPathList, "molecule::CreateListOfUniqueFragmentsOfOrder: *ShortestPathList");
-  Free((void **)&FragmentSearch.Labels, "molecule::CreateListOfUniqueFragmentsOfOrder: *Labels");
+  Free((void **)&FragmentSearch.BondsPerSPList, "molecule::PowerSetGenerator: ***BondsPerSPList");
+  Free((void **)&FragmentSearch.BondsPerSPCount, "molecule::PowerSetGenerator: *BondsPerSPCount");
+  Free((void **)&FragmentSearch.ShortestPathList, "molecule::PowerSetGenerator: *ShortestPathList");
+  Free((void **)&FragmentSearch.Labels, "molecule::PowerSetGenerator: *Labels");
   delete(FragmentSearch.FragmentSet);
   
-//  // gather all the leaves together
-//  *out << Verbose(0) << "Copying all fragments into MoleculeList structure." << endl; 
-//  FragmentList = new Graph;
-//  UniqueIndex = 0;
-//  while ((FragmentSearch.Leaflet != NULL) && (UniqueIndex < FragmentSearch.FragmentCounter))  {
-//    FragmentList->insert();
-//    FragmentList->ListOfMolecules[UniqueIndex++] = FragmentSearch.Leaflet->Leaf;
-//    FragmentSearch.Leaflet->Leaf = NULL; // prevent molecule from being removed
-//    TempLeaf = FragmentSearch.Leaflet;
-//    FragmentSearch.Leaflet = FragmentSearch.Leaflet->previous;
-//    delete(TempLeaf);
-//  };
-
   // return list  
-  *out << Verbose(0) << "End of CreateListOfUniqueFragmentsOfOrder." << endl;
+  *out << Verbose(0) << "End of PowerSetGenerator." << endl;
   return FragmentSearch.FragmentCounter;
 };
@@ -3664 +3440 @@
   GraphTestPair testGraphInsert;
 
-  testGraphInsert = Fragment->Leaflet->insert(GraphPair (*Fragment->FragmentSet,pair<int,double>(Fragment->FragmentCounter,Fragment->TEFactor)));  // store fragment number and current factor
+  testGraphInsert = Fragment->Leaflet->insert(GraphPair (*Fragment->FragmentSet,pair<int,double>(Fragment->FragmentCounter,1)));  // store fragment number and current factor
   if (testGraphInsert.second) {
     *out << Verbose(2) << "KeySet " << Fragment->FragmentCounter << " successfully inserted." << endl;
@@ -3670 +3446 @@
   } else {
     *out << Verbose(2) << "KeySet " << Fragment->FragmentCounter << " failed to insert, present fragment is " << ((*(testGraphInsert.first)).second).first << endl;
-    ((*(testGraphInsert.first)).second).second += Fragment->TEFactor;
+    ((*(testGraphInsert.first)).second).second ++;  // increase the "created" counter
     *out << Verbose(2) << "New factor is " << ((*(testGraphInsert.first)).second).second << "." << endl;
   }
@@ -3687 +3463 @@
  * \param graph1 first (dest) graph
  * \param graph2 second (source) graph
+ * \param *counter keyset counter that gets increased 
  */
 inline void InsertGraphIntoGraph(ofstream *out, Graph &graph1, Graph &graph2, int *counter)
@@ -3705 +3482 @@
 
 
-/** Creates truncated BOSSANOVA expansion up to order \a k.
+/** Performs BOSSANOVA decomposition at selected sites, increasing the cutoff by one at these sites.
+ * Important only is that we create all fragments, it is not important if we create them more than once
+ * as these copies are filtered out via use of the hash table (KeySet).
  * \param *out output stream for debugging
- * \param ANOVAOrder ANOVA expansion is truncated above this order
- * \param *configuration configuration for writing config files for each fragment
  * \return pointer to Graph list
  */
-Graph * molecule::FragmentBOSSANOVA(ofstream *out, int ANOVAOrder, config *configuration)
+Graph * molecule::FragmentBOSSANOVA(ofstream *out, KeyStack &RootStack)
 {
   Graph *FragmentList = NULL, ***FragmentLowerOrdersList = NULL;
-  //MoleculeListClass *FragmentMoleculeList = NULL;
   int Order, NumLevels, NumMolecules, TotalNumMolecules = 0, *NumMoleculesOfOrder = NULL;
   int counter = 0;
+  int UpgradeCount = RootStack.size();
+  KeyStack FragmentRootStack;
+  int RootKeyNr, RootNr;
   
   *out << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl;
@@ -3722 +3501 @@
   // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
   // with all needed lower orders that are subtracted, the other dimension is the BondOrder (i.e. from 1 to 5)
-  NumMoleculesOfOrder = (int *) Malloc(sizeof(int)*ANOVAOrder, "molecule::FragmentBOSSANOVA: *NumMoleculesOfOrder");
-  FragmentLowerOrdersList = (Graph ***) Malloc(sizeof(Graph **)*ANOVAOrder, "molecule::FragmentBOSSANOVA: ***FragmentLowerOrdersList");
-
-  // Construct the complete KeySet
+  NumMoleculesOfOrder = (int *) Malloc(sizeof(int)*UpgradeCount, "molecule::FragmentBOSSANOVA: *NumMoleculesOfOrder");
+  FragmentLowerOrdersList = (Graph ***) Malloc(sizeof(Graph **)*UpgradeCount, "molecule::FragmentBOSSANOVA: ***FragmentLowerOrdersList");
+
+  // Construct the complete KeySet which we need for topmost level only (but for all Roots)
   atom *Walker = start;
   KeySet CompleteMolecule;
@@ -3733 +3512 @@
   } 
 
-  for (int BondOrder=1;BondOrder<=ANOVAOrder;BondOrder++) {
-    // this can easily be seen: if Order is 5, then the number of levels for each lower order is the total sum of the number of levels above, as
-    // each has to be split up. E.g. for the second level we have one from 5th, one from 4th, two from 3th (which in turn is one from 5th, one from 4th),
-    // hence we have overall four 2th order levels for splitting. This also allows for putting all into a single array (FragmentLowerOrdersList[])
-    // with the order along the cells as this: 5433222211111111 for BondOrder 5 needing 16=pow(2,5-1) cells (only we use bit-shifting which is faster)
-    NumLevels = 1 << (BondOrder-1); // (int)pow(2,BondOrder-1);
-    *out << Verbose(0) << "BondOrder is (" << BondOrder << "/" << ANOVAOrder << ") and NumLevels is " << NumLevels << "." << endl;
-  
+  // this can easily be seen: if Order is 5, then the number of levels for each lower order is the total sum of the number of levels above, as
+  // each has to be split up. E.g. for the second level we have one from 5th, one from 4th, two from 3th (which in turn is one from 5th, one from 4th),
+  // hence we have overall four 2th order levels for splitting. This also allows for putting all into a single array (FragmentLowerOrdersList[])
+  // with the order along the cells as this: 5433222211111111 for BondOrder 5 needing 16=pow(2,5-1) cells (only we use bit-shifting which is faster)
+  RootNr = 0;   // counts through the roots in RootStack
+  while (RootNr < UpgradeCount) {
+    RootKeyNr = RootStack.front();
+    RootStack.pop_front();
+    // increase adaptive order by one
+    Walker = FindAtom(RootKeyNr);
+    Walker->GetTrueFather()->AdaptiveOrder++;
+    Order = Walker->AdaptiveOrder = Walker->GetTrueFather()->AdaptiveOrder;
+    
     // allocate memory for all lower level orders in this 1D-array of ptrs
-    FragmentLowerOrdersList[BondOrder-1] = (Graph **) Malloc(sizeof(Graph *)*NumLevels, "molecule::FragmentBOSSANOVA: **FragmentLowerOrdersList[]");
+    NumLevels = 1 << (Order); // (int)pow(2,Order);
+    FragmentLowerOrdersList[RootNr] = (Graph **) Malloc(sizeof(Graph *)*NumLevels, "molecule::FragmentBOSSANOVA: **FragmentLowerOrdersList[]");
   
     // create top order where nothing is reduced
     *out << Verbose(0) << "==============================================================================================================" << endl;
-    *out << Verbose(0) << "Creating list of unique fragments of Bond Order " << BondOrder << " itself." << endl;
+    *out << Verbose(0) << "Creating KeySets of Bond Order " << Order << " for " << *Walker << ", NumLevels is " << NumLevels << ", " << RootStack.size() << " Roots remaining." << endl;
+
     // Create list of Graphs of current Bond Order (i.e. F_{ij})
-    FragmentLowerOrdersList[BondOrder-1][0] =  new Graph;
-    NumMoleculesOfOrder[BondOrder-1] = CreateListOfUniqueFragmentsOfOrder(out, BondOrder, FragmentLowerOrdersList[BondOrder-1][0], CompleteMolecule, 1., configuration);
-    *out << Verbose(1) << "Number of resulting molecules is: " << NumMoleculesOfOrder[BondOrder-1] << "." << endl;
+    FragmentLowerOrdersList[RootNr][0] =  new Graph;
+    NumMoleculesOfOrder[RootNr] = PowerSetGenerator(out, Walker->AdaptiveOrder, FragmentLowerOrdersList[RootNr][0], CompleteMolecule, RootKeyNr);
+    *out << Verbose(1) << "Number of resulting KeySets is: " << NumMoleculesOfOrder[RootNr] << "." << endl;
     NumMolecules = 0;
     
-    // create lower order fragments
-    *out << Verbose(0) << "Creating list of unique fragments of lower Bond Order terms to be subtracted." << endl;
-    Order = BondOrder;
-    for (int source=0;source<(NumLevels >> 1);source++) { // 1-terms don't need any more splitting, that's why only half is gone through (shift again)
-
-      // step down to next order at (virtual) boundary of powers of 2 in array
-      while (source >= (1 << (BondOrder-Order))) // (int)pow(2,BondOrder-Order))    
-        Order--;
-      *out << Verbose(0) << "Current Order is: " << Order << "." << endl;
-      for (int SubOrder=Order;SubOrder>1;SubOrder--) {
-        int dest = source + (1 << (BondOrder-SubOrder));
-        *out << Verbose(0) << "--------------------------------------------------------------------------------------------------------------" << endl;
-        *out << Verbose(0) << "Current SubOrder is: " << SubOrder-1 << " with source " << source << " to destination " << dest << "." << endl;
-  
-        // every molecule is split into a list of again (Order - 1) molecules, while counting all molecules
-        //*out << Verbose(1) << "Splitting the " << (*FragmentLowerOrdersList[BondOrder-1][source]).size() << " molecules of the " << source << "th cell in the array." << endl;
-        //NumMolecules = 0;
-        FragmentLowerOrdersList[BondOrder-1][dest] = new Graph;
-        for(Graph::iterator runner = (*FragmentLowerOrdersList[BondOrder-1][source]).begin();runner != (*FragmentLowerOrdersList[BondOrder-1][source]).end(); runner++) {
-          NumMolecules += CreateListOfUniqueFragmentsOfOrder(out,SubOrder-1, FragmentLowerOrdersList[BondOrder-1][dest], (*runner).first, -(*runner).second.second, configuration);
+    if ((NumLevels >> 1) > 0) {
+      // create lower order fragments
+      *out << Verbose(0) << "Creating list of unique fragments of lower Bond Order terms to be subtracted." << endl;
+      Order = Walker->AdaptiveOrder;
+      for (int source=0;source<(NumLevels >> 1);source++) { // 1-terms don't need any more splitting, that's why only half is gone through (shift again)
+        // step down to next order at (virtual) boundary of powers of 2 in array
+        while (source >= (1 << (Walker->AdaptiveOrder-Order))) // (int)pow(2,Walker->AdaptiveOrder-Order))    
+          Order--;
+        *out << Verbose(0) << "Current Order is: " << Order << "." << endl;
+        for (int SubOrder=Order;SubOrder>1;SubOrder--) {
+          int dest = source + (1 << (Walker->AdaptiveOrder-SubOrder));
+          *out << Verbose(0) << "--------------------------------------------------------------------------------------------------------------" << endl;
+          *out << Verbose(0) << "Current SubOrder is: " << SubOrder-1 << " with source " << source << " to destination " << dest << "." << endl;
+    
+          // every molecule is split into a list of again (Order - 1) molecules, while counting all molecules
+          //*out << Verbose(1) << "Splitting the " << (*FragmentLowerOrdersList[RootNr][source]).size() << " molecules of the " << source << "th cell in the array." << endl;
+          //NumMolecules = 0;
+          FragmentLowerOrdersList[RootNr][dest] = new Graph;
+          for(Graph::iterator runner = (*FragmentLowerOrdersList[RootNr][source]).begin();runner != (*FragmentLowerOrdersList[RootNr][source]).end(); runner++) {
+            for (KeySet::iterator sprinter = (*runner).first.begin();sprinter != (*runner).first.end(); sprinter++) {
+              FragmentList = new Graph();
+              PowerSetGenerator(out, SubOrder-1, FragmentList, (*runner).first, *sprinter);
+              // insert new keysets FragmentList into FragmentLowerOrdersList[Walker->AdaptiveOrder-1][dest]
+              *out << Verbose(1) << "Merging resulting key sets with those present in destination " << dest << "." << endl;
+              InsertGraphIntoGraph(out, *FragmentLowerOrdersList[RootNr][dest], *FragmentList, &NumMolecules);
+              delete(FragmentList);
+            }
+          }
+          *out << Verbose(1) << "Number of resulting molecules for SubOrder " << SubOrder << " is: " << NumMolecules << "." << endl;
         }
-        *out << Verbose(1) << "Number of resulting molecules is: " << NumMolecules << "." << endl;
-      }
-    }
-    // now, we have completely filled each cell of FragmentLowerOrdersList[] for the current BondOrder
-    //NumMoleculesOfOrder[BondOrder-1] = NumMolecules;
-    TotalNumMolecules += NumMoleculesOfOrder[BondOrder-1];
-    *out << Verbose(1) << "Number of resulting molecules for Order " << BondOrder << " is: " << NumMoleculesOfOrder[BondOrder-1] << "." << endl;    
-  }
+      }
+    }
+    // now, we have completely filled each cell of FragmentLowerOrdersList[] for the current Walker->AdaptiveOrder
+    //NumMoleculesOfOrder[Walker->AdaptiveOrder-1] = NumMolecules;
+    TotalNumMolecules += NumMoleculesOfOrder[RootNr];
+    *out << Verbose(1) << "Number of resulting molecules for Order " << Walker->AdaptiveOrder << " is: " << NumMoleculesOfOrder[RootNr] << "." << endl;
+    RootStack.push_back(RootKeyNr); // put back on stack
+    RootNr++;
+  }
+  *out << Verbose(0) << "==============================================================================================================" << endl;
   *out << Verbose(1) << "Total number of resulting molecules is: " << TotalNumMolecules << "." << endl;
+  *out << Verbose(0) << "==============================================================================================================" << endl;
   // now, FragmentLowerOrdersList is complete, it looks - for BondOrder 5 - as this (number is the ANOVA Order of the terms therein) 
   // 5433222211111111
@@ -3789 +3587 @@
   // 21
   // 1
-  // Subsequently, we combine same orders into a single list (FragmentByOrderList) and reduce these by order
+  // Subsequently, we combine all into a single list (FragmentList)
 
   *out << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl;
   FragmentList = new Graph;
-  for (int BondOrder=1;BondOrder<=ANOVAOrder;BondOrder++) {
-    NumLevels = 1 << (BondOrder-1);
+  RootNr = 0;
+  while (!RootStack.empty()) {
+    RootKeyNr = RootStack.front();
+    RootStack.pop_front();
+    Walker = FindAtom(RootKeyNr); 
+    NumLevels = 1 << (Walker->AdaptiveOrder - 1);
     for(int i=0;i<NumLevels;i++) {
-      InsertGraphIntoGraph(out, *FragmentList, (*FragmentLowerOrdersList[BondOrder-1][i]), &counter);
-      delete(FragmentLowerOrdersList[BondOrder-1][i]);
-    }
-    Free((void **)&FragmentLowerOrdersList[BondOrder-1], "molecule::FragmentBOSSANOVA: **FragmentLowerOrdersList[]");
+      InsertGraphIntoGraph(out, *FragmentList, (*FragmentLowerOrdersList[RootNr][i]), &counter);
+      delete(FragmentLowerOrdersList[RootNr][i]);
+    }
+    Free((void **)&FragmentLowerOrdersList[RootNr], "molecule::FragmentBOSSANOVA: **FragmentLowerOrdersList[]");
+    RootNr++;
   }
   Free((void **)&FragmentLowerOrdersList, "molecule::FragmentBOSSANOVA: ***FragmentLowerOrdersList");
@@ -3807 +3610 @@
   return FragmentList;
 };
-
-/** Fragments a molecule, taking \a BondDegree neighbours into accent.
- * First of all, we have to split up the molecule into bonds ranging out till \a BondDegree.
- * These fragments serve in the following as the basis the calculate the bond energy of the bond
- * they originated from. Thus, they are split up in a left and a right part, each calculated for
- * the total energy, including the fragment as a whole and then we get: 
- * E(fragment) - E(left) - E(right) = E(bond)
- * The splitting up is done via Breadth-First-Search, \sa BreadthFirstSearchAdd().
- * \param *out output stream for debugging
- * \param BondOrder up to how many neighbouring bonds a fragment contains
- * \param *configuration configuration for writing config files for each fragment
- * \param CutCyclic whether to add cut cyclic bond or to saturate
- * \return pointer to MoleculeListClass with all the fragments or NULL if something went wrong.
- */
-MoleculeListClass * molecule::FragmentBottomUp(ofstream *out, int BondOrder, config *configuration, enum CutCyclicBond CutCyclic)
-{
-  int Num;
-  MoleculeListClass *FragmentList =  NULL, **FragmentsList = NULL;
-  bond *Bond = NULL;
-
-  *out << Verbose(0) << "Begin of FragmentBottomUp." << endl; 
-  FragmentsList = (MoleculeListClass **) Malloc(sizeof(MoleculeListClass *)*2, "molecule::FragmentBottomUp: **FragmentsList");
-  *out << Verbose(0) << "Getting Atomic fragments." << endl;
-  FragmentsList[0] = GetAtomicFragments(out, AtomCount, configuration->GetIsAngstroem(), 1., CutCyclic);
-
-  // create the fragments including each one bond of the original molecule and up to \a BondDegree neighbours
-  *out << Verbose(0) << "Getting " << 
-#ifdef ADDHYDROGEN  
-  NoNonBonds 
-#else
-  BondCount
-#endif
-                                        << " Bond fragments." << endl;
-  FragmentList = GetEachBondFragmentOfOrder(out, BondOrder, configuration->GetIsAngstroem(), CutCyclic);
-
-  // check whether there are equal fragments by ReduceToUniqueOnes
-  FragmentList->ReduceToUniqueList(out, &cell_size[0], BondDistance);
-
-        *out << Verbose(0) << "Begin of Separating " << FragmentList->NumberOfMolecules << " Fragments into Bond pieces." << endl;
-        // as we have the list, we have to take each fragment split it relative to its originating
-        // bond into left and right and store these in a new list
-  *out << Verbose(2) << endl << "Allocating MoleculeListClass" << endl; 
-  FragmentsList[1] =  new MoleculeListClass(3*FragmentList->NumberOfMolecules, AtomCount); // for each molecule the whole and its left and right part 
-  *out << Verbose(2) << "Creating TEList." << endl; 
-  // and create TE summation for these bond energy approximations (bond = whole - left - right)
-  for(int i=0;i<FragmentList->NumberOfMolecules;i++) {
-    // make up factors to regain total energy of whole molecule
-    FragmentsList[1]->TEList[3*i] = FragmentList->TEList[i];       // bond energy is 1 * whole 
-    FragmentsList[1]->TEList[3*i+1] = -FragmentList->TEList[i];    // - 1. * left part
-    FragmentsList[1]->TEList[3*i+2] = -FragmentList->TEList[i];    // - 1. * right part
-
-    // shift the pointer on whole molecule to new list in order to avoid that this molecule is deleted on deconstructing FragmentList
-    FragmentsList[1]->ListOfMolecules[3*i] = FragmentList->ListOfMolecules[i]; 
-    *out << Verbose(2) << "shifting whole fragment pointer for fragment " << FragmentList->ListOfMolecules[i] << " -> " <<  FragmentsList[1]->ListOfMolecules[3*i] << "." << endl;
-    // create bond matrix and count bonds
-    *out << Verbose(2) << "Updating bond list for fragment " << i << " [" << FragmentList << "]: " << FragmentList->ListOfMolecules[i] << endl; 
-    // create list of bonds per atom for this fragment (atoms were counted above)
-    FragmentsList[1]->ListOfMolecules[3*i]->CreateListOfBondsPerAtom(out);
-     
-    *out << Verbose(0) << "Getting left & right fragments for fragment " << i << "." << endl;
-    // the bond around which the fragment has been setup is always the first by construction (bond partners are first added atoms)
-    Bond = FragmentsList[1]->ListOfMolecules[3*i]->first->next; // is the bond between atom 0 and another in the middle
-    FragmentsList[1]->ListOfMolecules[3*i]->FragmentMoleculeByBond(out, Bond, &(FragmentsList[1]->ListOfMolecules[3*i+1]), &(FragmentsList[1]->ListOfMolecules[3*i+2]), configuration->GetIsAngstroem(), CutCyclic);
-    if ((FragmentsList[1]->ListOfMolecules[3*i+1] == NULL) || (FragmentsList[1]->ListOfMolecules[3*i+2] == NULL)) {
-      *out << Verbose(2) << "Left and/or Right Fragment is NULL!" << endl;
-    } else {
-      *out << Verbose(3) << "Left Fragment is " <<  FragmentsList[1]->ListOfMolecules[3*i+1] << ": " << endl;
-      FragmentsList[1]->ListOfMolecules[3*i+1]->Output(out);
-      *out << Verbose(3) << "Right Fragment is " <<  FragmentsList[1]->ListOfMolecules[3*i+2] << ": " << endl;
-      FragmentsList[1]->ListOfMolecules[3*i+2]->Output(out);
-      *out << endl;
-    }
-    // remove in old list, so that memory for this molecule is not free'd on final delete of this list
-    FragmentList->ListOfMolecules[i] = NULL;
-  }
-        *out << Verbose(0) << "End of Separating Fragments into Bond pieces." << endl;
-  delete(FragmentList);
-  FragmentList = NULL;
-
-  // combine atomic and bond list
-  FragmentList = new MoleculeListClass(FragmentsList[0]->NumberOfMolecules + FragmentsList[1]->NumberOfMolecules, AtomCount);
-  Num = 0;
-  for(int i=0;i<2;i++) {
-    for(int j=0;j<FragmentsList[i]->NumberOfMolecules;j++) {
-      // transfer molecule
-      FragmentList->ListOfMolecules[Num] = FragmentsList[i]->ListOfMolecules[j];
-      FragmentsList[i]->ListOfMolecules[j] = NULL;
-      // transfer TE factor
-      FragmentList->TEList[Num] = FragmentsList[i]->TEList[j];
-      Num++;
-    }
-    delete(FragmentsList[i]);
-    FragmentsList[i] = NULL;
-  }
-  *out << Verbose(2) << "Memory cleanup and return with filled list." << endl; 
-  Free((void **)&FragmentsList, "molecule::FragmentBottomUp: **FragmentsList");
-
-  // reducing list
-  FragmentList->ReduceToUniqueList(out, &cell_size[0], BondDistance);
-        
-        // write configs for all fragements (are written in FragmentMolecule)
-  // free FragmentList
-  *out << Verbose(0) << "End of FragmentBottomUp." << endl; 
-  return FragmentList;
-};
-
 
 /** Comparision function for GSL heapsort on distances in two molecules.