Changeset 339910

Timestamp:

Dec 3, 2012, 9:49:30 AM (12 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

de0af2

Parents:

b9401e

git-author:

Frederik Heber <heber@…> (09/19/12 14:32:32)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:30)

Message:

Fragmentation now operates on a single molecule.

• FragmentMolecule() does not continue on Subgraphs.
• shifted remaining functionality from MoleculeLeafClass to Fragmentation.
• FragmentList, KeySets, and RootStack are all just instances not arrays anymore.

Location:

src

Files:

• Fragmentation/Fragmentation.cpp (modified) (12 diffs)
• Fragmentation/Fragmentation.hpp (modified) (3 diffs)
• Fragmentation/fragmentation_helpers.cpp (modified) (3 diffs)
• Fragmentation/fragmentation_helpers.hpp (modified) (1 diff)
• MoleculeLeafClass.cpp (modified) (1 diff)
• MoleculeLeafClass.hpp (modified) (1 diff)

src/Fragmentation/Fragmentation.cpp

@@ -103 +103 @@
 {
   MoleculeListClass *BondFragments = NULL;
-  int FragmentCounter;
-  MoleculeLeafClass *MolecularWalker = NULL;
-  MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
-  fstream File;
+  std::fstream File;
   bool FragmentationToDo = true;
   bool CheckOrder = false;
-  Graph **FragmentList = NULL;
   Graph TotalGraph;     // graph with all keysets however local numbers
   int TotalNumberOfKeySets = 0;
   AtomMask_t AtomMask(atomids);
 
-  LOG(0, endl);
+  LOG(0, std::endl);
   switch (saturation) {
     case DoSaturate:
@@ -137 +133 @@
   }
 
-  // ===== 2. perform a DFS analysis to gather info on cyclic structure and a list of disconnected subgraphs =====
-  // NOTE: We assume here that DFS has been performed and molecule structure is current.
-  Subgraphs = DFS.getMoleculeStructure();
-
   // ===== 3. if structure still valid, parse key set file and others =====
   Graph ParsedFragmentList;
@@ -150 +142 @@
   // =================================== Begin of FRAGMENTATION ===============================
   // ===== 6a. assign each keyset to its respective subgraph =====
-  const int MolCount = World::getInstance().numMolecules();
-  FragmentCounter = 0;
-  {
-    ListOfLocalAtoms_t *ListOfLocalAtoms = new ListOfLocalAtoms_t[MolCount];
-    Subgraphs->next->AssignKeySetsToFragment(mol, &ParsedFragmentList, ListOfLocalAtoms, FragmentList, FragmentCounter, true);
-    delete[] ListOfLocalAtoms;
-  }
+  ListOfLocalAtoms_t ListOfLocalAtoms;
+  Graph FragmentList;
+  AssignKeySetsToFragment(ParsedFragmentList, ListOfLocalAtoms, FragmentList, true);
 
   // ===== 6b. prepare and go into the adaptive (Order<0), single-step (Order==0) or incremental (Order>0) cycle
-  KeyStack *RootStack = new KeyStack[Subgraphs->next->Count()];
+  KeyStack RootStack;
   FragmentationToDo = false;  // if CheckOrderAtSite just ones recommends fragmentation, we will save fragments afterwards
   bool LoopDoneAlready = false;
-  while ((CheckOrder = CheckOrderAtSite(AtomMask, &ParsedFragmentList, Order, prefix, LoopDoneAlready))) {
+  while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, prefix, LoopDoneAlready))) {
     FragmentationToDo = FragmentationToDo || CheckOrder;
     LoopDoneAlready = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
     // ===== 6b. fill RootStack for each subgraph (second adaptivity check) =====
-    Subgraphs->next->FillRootStackForSubgraphs(RootStack, AtomMask, (FragmentCounter = 0), saturation);
-
-    // ===== 7. fill the bond fragment list =====
-    FragmentCounter = 0;
-    MolecularWalker = Subgraphs;
-    while (MolecularWalker->next != NULL) {
-      MolecularWalker = MolecularWalker->next;
-      LOG(1, "Fragmenting subgraph " << MolecularWalker << ".");
-      if (MolecularWalker->Leaf->hasBondStructure()) {
-        // call BOSSANOVA method
-        LOG(0, endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= ");
-        FragmentBOSSANOVA(MolecularWalker->Leaf, FragmentList[FragmentCounter], RootStack[FragmentCounter]);
-      } else {
-        ELOG(1, "Subgraph " << MolecularWalker << " has no atoms!");
-      }
-      FragmentCounter++;  // next fragment list
-    }
+    FillRootStackForSubgraphs(RootStack, AtomMask);
+
+    // call BOSSANOVA method
+    FragmentBOSSANOVA(mol, FragmentList, RootStack);
   }
   LOG(2, "CheckOrder is " << CheckOrder << ".");
-  delete[](RootStack);
 
   // ==================================== End of FRAGMENTATION ============================================
 
   // ===== 8a. translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
-  Subgraphs->next->TranslateIndicesToGlobalIDs(FragmentList, (FragmentCounter = 0), TotalNumberOfKeySets, TotalGraph);
-
-  // free subgraph memory again
-  FragmentCounter = 0;
-  while (Subgraphs != NULL) {
-    // remove entry in fragment list
-    // remove subgraph fragment
-    MolecularWalker = Subgraphs->next;
-    Subgraphs->Leaf = NULL;
-    delete(Subgraphs);
-    Subgraphs = MolecularWalker;
-  }
-  // free fragment list
-  for (int i=0; i< FragmentCounter; ++i )
-    delete(FragmentList[i]);
-  delete[](FragmentList);
-
-  LOG(0, FragmentCounter << " subgraph fragments have been removed.");
+  TranslateIndicesToGlobalIDs(FragmentList, TotalNumberOfKeySets, TotalGraph);
 
   // ===== 8b. gather keyset lists (graphs) from all subgraphs and transform into MoleculeListClass =====
@@ -300 +257 @@
  * \return pointer to Graph list
  */
-void Fragmentation::FragmentBOSSANOVA(molecule *mol, Graph *&FragmentList, KeyStack &RootStack)
-{
+void Fragmentation::FragmentBOSSANOVA(molecule *mol, Graph &FragmentList, KeyStack &RootStack)
+{
+  Info FunctionInfo(__func__);
   Graph ***FragmentLowerOrdersList = NULL;
   int NumLevels = 0;
@@ -313 +271 @@
   int RootNr = 0;
   UniqueFragments FragmentSearch;
-
-  LOG(0, "Begin of FragmentBOSSANOVA.");
 
   // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
@@ -403 +359 @@
   FreeAllOrdersList(FragmentLowerOrdersList, RootStack, mol);
   delete[](NumMoleculesOfOrder);
-
-  LOG(0, "End of FragmentBOSSANOVA.");
 };
 
@@ -465 +419 @@
  * \return true - needs further fragmentation, false - does not need fragmentation
  */
-bool Fragmentation::CheckOrderAtSite(AtomMask_t &AtomMask, Graph *GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready)
+bool Fragmentation::CheckOrderAtSite(AtomMask_t &AtomMask, const Graph &GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready)
 {
   bool status = false;
@@ -477 +431 @@
 
     // transmorph graph keyset list into indexed KeySetList
-    if (GlobalKeySetList == NULL) {
-      ELOG(1, "Given global key set list (graph) is NULL!");
-      return false;
-    }
-    AdaptivityMap * IndexKeySetList = GlobalKeySetList->GraphToAdaptivityMap();
+    AdaptivityMap * IndexKeySetList = GlobalKeySetList.GraphToAdaptivityMap();
 
     // parse the EnergyPerFragment file
@@ -562 +512 @@
 bool Fragmentation::ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, std::string &path)
 {
+  Info FunctionInfo(__func__);
   typedef unsigned char order_t;
   typedef std::map<atomId_t, order_t> OrderArray_t;
@@ -571 +522 @@
   ifstream file;
 
-  LOG(1, "Begin of ParseOrderAtSiteFromFile");
   line = path + ORDERATSITEFILE;
   file.open(line.c_str());
@@ -603 +553 @@
   }
 
-  LOG(1, "End of ParseOrderAtSiteFromFile");
   return status;
 };
@@ -729 +678 @@
   typelist = types;
 }
+
+/** Fills the root stack for sites to be used as root in fragmentation depending on order or adaptivity criteria
+ * Again, as in \sa FillBondStructureFromReference steps recursively through each Leaf in this chain list of molecule's.
+ * \param &RootStack stack to be filled
+ * \param AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site
+ * \return true - stack is non-empty, fragmentation necessary, false - stack is empty, no more sites to update
+ */
+void Fragmentation::FillRootStackForSubgraphs(KeyStack &RootStack, const AtomMask_t &AtomMask)
+{
+  for(molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    const atom * const Father = (*iter)->GetTrueFather();
+    if (AtomMask.isTrue(Father->getNr())) // apply mask
+      if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
+        RootStack.push_front((*iter)->getNr());
+  }
+}
+
+/** The indices per keyset are compared to the respective father's Atom::Nr in each subgraph and thus put into \a **&FragmentList.
+ * \param *KeySetList list with all keysets
+ * \param ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
+ * \param **&FragmentList list to be allocated and returned
+ * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
+ * \retuen true - success, false - failure
+ */
+bool Fragmentation::AssignKeySetsToFragment(Graph &KeySetList, ListOfLocalAtoms_t &ListOfLocalAtoms, Graph &FragmentList, bool FreeList)
+{
+  Info FunctionInfo(__func__);
+  bool status = true;
+  size_t KeySetCounter = 0;
+
+  // fill ListOfLocalAtoms if NULL was given
+  if (!mol->FillListOfLocalAtoms(ListOfLocalAtoms, mol->getAtomCount())) {
+    LOG(1, "Filling of ListOfLocalAtoms failed.");
+    return false;
+  }
+
+  if (KeySetList.size() != 0) { // if there are some scanned keysets at all
+    // assign scanned keysets
+    KeySet TempSet;
+    for (Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++) { // key sets contain global numbers!
+      if (ListOfLocalAtoms[mol->FindAtom(*((*runner).first.begin()))->getNr()] != NULL) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
+        // translate keyset to local numbers
+        for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
+          TempSet.insert(ListOfLocalAtoms[mol->FindAtom(*sprinter)->getNr()]->getNr());
+        // insert into FragmentList
+        FragmentList.insert(GraphPair(TempSet, pair<int, double> (KeySetCounter++, (*runner).second.second)));
+      }
+      TempSet.clear();
+    }
+  } else
+    LOG(1, "KeySetList is NULL or empty.");
+
+  if (FreeList) {
+    // free the index lookup list
+    ListOfLocalAtoms.clear();
+  }
+  return status;
+}
+
+/** Translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
+ * \param &FragmentList Graph with local numbers per fragment
+ * \param &TotalNumberOfKeySets global key set counter
+ * \param &TotalGraph Graph to be filled with global numbers
+ */
+void Fragmentation::TranslateIndicesToGlobalIDs(Graph &FragmentList, int &TotalNumberOfKeySets, Graph &TotalGraph)
+{
+  Info FunctionInfo(__func__);
+  for (Graph::iterator runner = FragmentList.begin(); runner != FragmentList.end(); runner++) {
+    KeySet TempSet;
+    for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
+      TempSet.insert((mol->FindAtom(*sprinter))->GetTrueFather()->getNr());
+    TotalGraph.insert(GraphPair(TempSet, pair<int, double> (TotalNumberOfKeySets++, (*runner).second.second)));
+  }
+}
+

src/Fragmentation/Fragmentation.hpp

@@ -43 +43 @@
 private:
 
-  void FragmentBOSSANOVA(molecule *mol, Graph *&FragmentList, KeyStack &RootStack);
+  void FragmentBOSSANOVA(molecule *mol, Graph &FragmentList, KeyStack &RootStack);
   int GuesstimateFragmentCount(int order);
 
@@ -49 +49 @@
 
   // order at site
-  bool CheckOrderAtSite(AtomMask_t &AtomMask, Graph *GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready);
+  bool CheckOrderAtSite(AtomMask_t &AtomMask, const Graph &GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready);
   bool StoreOrderAtSiteFile(std::string &path);
   bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, std::string &path);
@@ -57 +57 @@
   int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
   void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);
+  void FillRootStackForSubgraphs(KeyStack &RootStack, const AtomMask_t &AtomMask);
+  bool AssignKeySetsToFragment(Graph &KeySetList, ListOfLocalAtoms_t &ListOfLocalAtoms, Graph &FragmentList, bool FreeList = false);
+  void TranslateIndicesToGlobalIDs(Graph &FragmentList, int &TotalNumberOfKeySets, Graph &TotalGraph);
 
 private:

src/Fragmentation/fragmentation_helpers.cpp

@@ -77 +77 @@
 
 /** Combines all KeySets from all orders into single ones (with just unique entries).
- * \param *out output stream for debugging
- * \param *&FragmentList list to fill
+ * \param &FragmentList list to fill
  * \param ***FragmentLowerOrdersList
  * \param &RootStack stack with all root candidates (unequal to each atom in complete molecule if adaptive scheme is applied)
  * \param *mol molecule with atoms and bonds
  */
-int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
+int CombineAllOrderListIntoOne(Graph &FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
 {
   int RootNr = 0;
@@ -93 +92 @@
 
   LOG(0, "Combining the lists of all orders per order and finally into a single one.");
-  if (FragmentList == NULL) {
-    FragmentList = new Graph;
-    counter = 0;
-  } else {
-    counter = FragmentList->size();
-  }
+  counter = FragmentList.size();
 
   StartNr = RootStack.back();
@@ -108 +102 @@
     for(int i=0;i<NumLevels;i++) {
       if (FragmentLowerOrdersList[RootNr][i] != NULL) {
-        (*FragmentList).InsertGraph((*FragmentLowerOrdersList[RootNr][i]), &counter);
+        FragmentList.InsertGraph((*FragmentLowerOrdersList[RootNr][i]), &counter);
       }
     }

src/Fragmentation/fragmentation_helpers.hpp

@@ -31 +31 @@
 void PrintAtomMask(const AtomMask_t &AtomMask, int AtomCount);
 
-int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);
+int CombineAllOrderListIntoOne(Graph &FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);
 void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);
 

src/MoleculeLeafClass.cpp

@@ -116 +116 @@
 };
 
-/** Fills the root stack for sites to be used as root in fragmentation depending on order or adaptivity criteria
- * Again, as in \sa FillBondStructureFromReference steps recursively through each Leaf in this chain list of molecule's.
- * \param *out output stream for debugging
- * \param *&RootStack stack to be filled
- * \param AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site
- * \param &FragmentCounter counts through the fragments in this MoleculeLeafClass
- * \param saturation whether to treat hydrogen special or not
- * \return true - stack is non-empty, fragmentation necessary, false - stack is empty, no more sites to update
- */
-bool MoleculeLeafClass::FillRootStackForSubgraphs(KeyStack *&RootStack, const AtomMask_t &AtomMask, int &FragmentCounter, const enum HydrogenSaturation saturation)
-{
-  if (RootStack != NULL) {
-    // find first root candidates
-    if (&(RootStack[FragmentCounter]) != NULL) {
-      RootStack[FragmentCounter].clear();
-      for(molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ++iter) {
-        const atom * const Father = (*iter)->GetTrueFather();
-        if (AtomMask.isTrue(Father->getNr())) // apply mask
-          if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
-            RootStack[FragmentCounter].push_front((*iter)->getNr());
-      }
-      if (next != NULL)
-        next->FillRootStackForSubgraphs(RootStack, AtomMask, ++FragmentCounter, saturation);
-    } else {
-      LOG(1, "Rootstack[" << FragmentCounter << "] is NULL.");
-      return false;
-    }
-    FragmentCounter--;
-    return true;
-  } else {
-    LOG(1, "Rootstack is NULL.");
-    return false;
-  }
-};
 
-/** The indices per keyset are compared to the respective father's Atom::Nr in each subgraph and thus put into \a **&FragmentList.
- * \param *out output stream fro debugging
- * \param *reference reference molecule with the bond structure to be copied
- * \param *KeySetList list with all keysets
- * \param *ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
- * \param **&FragmentList list to be allocated and returned
- * \param &FragmentCounter counts the fragments as we move along the list
- * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
- * \retuen true - success, false - failure
- */
-bool MoleculeLeafClass::AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, ListOfLocalAtoms_t *&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList)
-{
-  bool status = true;
-  int KeySetCounter = 0;
-
-  LOG(1, "Begin of AssignKeySetsToFragment.");
-  // fill ListOfLocalAtoms if NULL was given
-  if (!Leaf->FillListOfLocalAtoms(ListOfLocalAtoms[FragmentCounter], reference->getAtomCount())) {
-    LOG(1, "Filling of ListOfLocalAtoms failed.");
-    return false;
-  }
-
-  // allocate fragment list
-  if (FragmentList == NULL) {
-    KeySetCounter = Count();
-    FragmentList = new Graph*[KeySetCounter];
-    for (int i=0;i<KeySetCounter;i++)
-      FragmentList[i] = NULL;
-    KeySetCounter = 0;
-  }
-
-  if ((KeySetList != NULL) && (KeySetList->size() != 0)) { // if there are some scanned keysets at all
-    // assign scanned keysets
-    if (FragmentList[FragmentCounter] == NULL)
-      FragmentList[FragmentCounter] = new Graph;
-    KeySet *TempSet = new KeySet;
-    for (Graph::iterator runner = KeySetList->begin(); runner != KeySetList->end(); runner++) { // key sets contain global numbers!
-      if (ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->getNr()] != NULL) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
-        // translate keyset to local numbers
-        for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
-          TempSet->insert(ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*sprinter)->getNr()]->getNr());
-        // insert into FragmentList
-        FragmentList[FragmentCounter]->insert(GraphPair(*TempSet, pair<int, double> (KeySetCounter++, (*runner).second.second)));
-      }
-      TempSet->clear();
-    }
-    delete (TempSet);
-    if (KeySetCounter == 0) {// if there are no keysets, delete the list
-      LOG(1, "KeySetCounter is zero, deleting FragmentList.");
-      delete (FragmentList[FragmentCounter]);
-    } else
-      LOG(1, KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << ".");
-    FragmentCounter++;
-    if (next != NULL)
-      next->AssignKeySetsToFragment(reference, KeySetList, ListOfLocalAtoms, FragmentList, FragmentCounter, FreeList);
-    FragmentCounter--;
-  } else
-    LOG(1, "KeySetList is NULL or empty.");
-
-  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
-    // free the index lookup list
-    (ListOfLocalAtoms[FragmentCounter]).clear();
-  }
-  LOG(1, "End of AssignKeySetsToFragment.");
-  return status;
-};
-
-/** Translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
- * \param *out output stream for debugging
- * \param **FragmentList Graph with local numbers per fragment
- * \param &FragmentCounter counts the fragments as we move along the list
- * \param &TotalNumberOfKeySets global key set counter
- * \param &TotalGraph Graph to be filled with global numbers
- */
-void MoleculeLeafClass::TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
-{
-  LOG(1, "Begin of TranslateIndicesToGlobalIDs.");
-  KeySet *TempSet = new KeySet;
-  if (FragmentList[FragmentCounter] != NULL) {
-    for (Graph::iterator runner = FragmentList[FragmentCounter]->begin(); runner != FragmentList[FragmentCounter]->end(); runner++) {
-      for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
-        TempSet->insert((Leaf->FindAtom(*sprinter))->GetTrueFather()->getNr());
-      TotalGraph.insert(GraphPair(*TempSet, pair<int, double> (TotalNumberOfKeySets++, (*runner).second.second)));
-      TempSet->clear();
-    }
-    delete (TempSet);
-  } else {
-    LOG(1, "FragmentList is NULL.");
-  }
-  if (next != NULL)
-    next->TranslateIndicesToGlobalIDs(FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
-  FragmentCounter--;
-  LOG(1, "End of TranslateIndicesToGlobalIDs.");
-};
 
 /** Simply counts the number of items in the list, from given MoleculeLeafClass.

src/MoleculeLeafClass.hpp

@@ -40 +40 @@
 
   bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
-  bool FillRootStackForSubgraphs(KeyStack *&RootStack, const AtomMask_t &AtomMask, int &FragmentCounter, const enum HydrogenSaturation saturation);
-  bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, ListOfLocalAtoms_t *&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
-  void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
   int Count() const;
 };