Changes in src/molecule_graph.cpp [68f03d:112b09]

File:

• src/molecule_graph.cpp (modified) (42 diffs)

src/molecule_graph.cpp

@@ -5 +5 @@
  *      Author: heber
  */
+
+#include "Helpers/MemDebug.hpp"
 
 #include "atom.hpp"
@@ -12 +14 @@
 #include "element.hpp"
 #include "helpers.hpp"
+#include "info.hpp"
 #include "linkedcell.hpp"
 #include "lists.hpp"
@@ -19 +22 @@
 #include "World.hpp"
 #include "Helpers/fast_functions.hpp"
+#include "Helpers/Assert.hpp"
+
 
 struct BFSAccounting
@@ -54 +59 @@
 void molecule::CreateAdjacencyListFromDbondFile(ifstream *input)
 {
-
+  Info FunctionInfo(__func__);
   // 1 We will parse bonds out of the dbond file created by tremolo.
   int atom1, atom2;
   atom *Walker, *OtherWalker;
-
-  if (!input) {
-    DoLog(1) && (Log() << Verbose(1) << "Opening silica failed \n");
+  char line[MAXSTRINGSIZE];
+
+  if (input->fail()) {
+    DoeLog(0) && (eLog() << Verbose(0) << "Opening of bond file failed \n");
+    performCriticalExit();
   };
-
-  *input >> ws >> atom1;
-  *input >> ws >> atom2;
-  DoLog(1) && (Log() << Verbose(1) << "Scanning file\n");
+  doCountAtoms();
+
+  // skip header
+  input->getline(line,MAXSTRINGSIZE);
+  DoLog(1) && (Log() << Verbose(1) << "Scanning file ... \n");
   while (!input->eof()) // Check whether we read everything already
   {
-    *input >> ws >> atom1;
-    *input >> ws >> atom2;
-
+    input->getline(line,MAXSTRINGSIZE);
+    stringstream zeile(line);
+    zeile >> atom1;
+    zeile >> atom2;
+
+    DoLog(2) && (Log() << Verbose(2) << "Looking for atoms " << atom1 << " and " << atom2 << "." << endl);
     if (atom2 < atom1) //Sort indices of atoms in order
       flip(atom1, atom2);
     Walker = FindAtom(atom1);
+    ASSERT(Walker,"Could not find an atom with the ID given in dbond file");
     OtherWalker = FindAtom(atom2);
+    ASSERT(OtherWalker,"Could not find an atom with the ID given in dbond file");
     AddBond(Walker, OtherWalker); //Add the bond between the two atoms with respective indices.
   }
@@ -103 +116 @@
   atom *Walker = NULL;
   atom *OtherWalker = NULL;
-  atom **AtomMap = NULL;
   int n[NDIM];
   double MinDistance, MaxDistance;
@@ -118 +130 @@
   DoLog(0) && (Log() << Verbose(0) << "Begin of CreateAdjacencyList." << endl);
   // remove every bond from the list
-  bond *Binder = NULL;
-  while (last->previous != first) {
-    Binder = last->previous;
-    Binder->leftatom->UnregisterBond(Binder);
-    Binder->rightatom->UnregisterBond(Binder);
-    removewithoutcheck(Binder);
-  }
+  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+      if ((*BondRunner)->leftatom == *AtomRunner)
+        delete((*BondRunner));
   BondCount = 0;
 
   // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)
-  CountAtoms();
-  DoLog(1) && (Log() << Verbose(1) << "AtomCount " << AtomCount << " and bonddistance is " << bonddistance << "." << endl);
-
-  if ((AtomCount > 1) && (bonddistance > 1.)) {
+  DoLog(1) && (Log() << Verbose(1) << "AtomCount " << getAtomCount() << " and bonddistance is " << bonddistance << "." << endl);
+
+  if ((getAtomCount() > 1) && (bonddistance > 1.)) {
     DoLog(2) && (Log() << Verbose(2) << "Creating Linked Cell structure ... " << endl);
     LC = new LinkedCell(this, bonddistance);
@@ -137 +145 @@
     // create a list to map Tesselpoint::nr to atom *
     DoLog(2) && (Log() << Verbose(2) << "Creating TesselPoint to atom map ... " << endl);
-    AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
-    Walker = start;
-    while (Walker->next != end) {
-      Walker = Walker->next;
-      AtomMap[Walker->nr] = Walker;
+
+    // set numbers for atoms that can later be used
+    int i=0;
+    for(internal_iterator iter = atoms.begin();iter!= atoms.end(); ++iter){
+      (*iter)->nr = i++;
     }
 
@@ -153 +161 @@
           if (List != NULL) {
             for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
-              Walker = AtomMap[(*Runner)->nr];
-//              Log() << Verbose(0) << "Current Atom is " << *Walker << "." << endl;
+              Walker = dynamic_cast<atom*>(*Runner);
+              ASSERT(Walker,"Tesselpoint that was not an atom retrieved from LinkedNode");
+              //Log() << Verbose(0) << "Current Atom is " << *Walker << "." << endl;
               // 3c. check for possible bond between each atom in this and every one in the 27 cells
               for (n[0] = -1; n[0] <= 1; n[0]++)
@@ -164 +173 @@
                       for (LinkedCell::LinkedNodes::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
                         if ((*OtherRunner)->nr > Walker->nr) {
-                          OtherWalker = AtomMap[(*OtherRunner)->nr];
-//                          Log() << Verbose(0) << "Current other Atom is " << *OtherWalker << "." << endl;
-                          const double distance = OtherWalker->x.PeriodicDistanceSquared(Walker->x, cell_size);
-//                          Log() << Verbose(1) << "Checking distance " << distance << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
+                          OtherWalker = dynamic_cast<atom*>(*OtherRunner);
+                          ASSERT(OtherWalker,"TesselPoint that was not an atom retrieved from LinkedNode");
+                          //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
                           (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+                          const double distance = OtherWalker->x.PeriodicDistanceSquared(Walker->x,cell_size);
                           const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
 //                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;
@@ -188 +197 @@
           }
         }
-    Free(&AtomMap);
     delete (LC);
     DoLog(1) && (Log() << Verbose(1) << "I detected " << BondCount << " bonds in the molecule with distance " << BondDistance << "." << endl);
@@ -199 +207 @@
     ActOnAllAtoms( &atom::OutputBondOfAtom );
   } else
-    DoLog(1) && (Log() << Verbose(1) << "AtomCount is " << AtomCount << ", thus no bonds, no connections!." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "AtomCount is " << getAtomCount() << ", thus no bonds, no connections!." << endl);
   DoLog(0) && (Log() << Verbose(0) << "End of CreateAdjacencyList." << endl);
   if (free_BG)
@@ -206 +214 @@
 ;
 
+/** Checks for presence of bonds within atom list.
+ * TODO: more sophisticated check for bond structure (e.g. connected subgraph, ...)
+ * \return true - bonds present, false - no bonds
+ */
+bool molecule::hasBondStructure()
+{
+  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    if (!(*AtomRunner)->ListOfBonds.empty())
+      return true;
+  return false;
+}
+
+/** Counts the number of present bonds.
+ * \return number of bonds
+ */
+unsigned int molecule::CountBonds() const
+{
+  unsigned int counter = 0;
+  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+      if ((*BondRunner)->leftatom == *AtomRunner)
+        counter++;
+  return counter;
+}
+
 /** Prints a list of all bonds to \a *out.
  * \param output stream
@@ -212 +245 @@
 {
   DoLog(1) && (Log() << Verbose(1) << endl << "From contents of bond chain list:");
-  bond *Binder = first;
-  while (Binder->next != last) {
-    Binder = Binder->next;
-    DoLog(0) && (Log() << Verbose(0) << *Binder << "\t" << endl);
-  }
+  for(molecule::const_iterator AtomRunner = molecule::begin(); AtomRunner != molecule::end(); ++AtomRunner)
+    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+      if ((*BondRunner)->leftatom == *AtomRunner) {
+        DoLog(0) && (Log() << Verbose(0) << *(*BondRunner) << "\t" << endl);
+      }
   DoLog(0) && (Log() << Verbose(0) << endl);
 }
@@ -241 +274 @@
     DoLog(0) && (Log() << Verbose(0) << " done." << endl);
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "BondCount is " << BondCount << ", no bonds between any of the " << AtomCount << " atoms." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "BondCount is " << BondCount << ", no bonds between any of the " << getAtomCount() << " atoms." << endl);
   }
   DoLog(0) && (Log() << Verbose(0) << No << " bonds could not be corrected." << endl);
@@ -260 +293 @@
   MoleculeLeafClass *Subgraphs = NULL;
   class StackClass<bond *> *BackEdgeStack = NULL;
-  bond *Binder = first;
-  if ((Binder->next != last) && (Binder->next->Type == Undetermined)) {
-    DoLog(0) && (Log() << Verbose(0) << "No Depth-First-Search analysis performed so far, calling ..." << endl);
-    Subgraphs = DepthFirstSearchAnalysis(BackEdgeStack);
-    while (Subgraphs->next != NULL) {
-      Subgraphs = Subgraphs->next;
-      delete (Subgraphs->previous);
-    }
-    delete (Subgraphs);
-    delete[] (MinimumRingSize);
-  }
-  while (Binder->next != last) {
-    Binder = Binder->next;
-    if (Binder->Cyclic)
-      NoCyclicBonds++;
-  }
+  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    if ((!(*AtomRunner)->ListOfBonds.empty()) && ((*(*AtomRunner)->ListOfBonds.begin())->Type == Undetermined)) {
+      DoLog(0) && (Log() << Verbose(0) << "No Depth-First-Search analysis performed so far, calling ..." << endl);
+      Subgraphs = DepthFirstSearchAnalysis(BackEdgeStack);
+      while (Subgraphs->next != NULL) {
+        Subgraphs = Subgraphs->next;
+        delete (Subgraphs->previous);
+      }
+      delete (Subgraphs);
+      delete[] (MinimumRingSize);
+      break;
+    }
+  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+      if ((*BondRunner)->leftatom == *AtomRunner)
+        if ((*BondRunner)->Cyclic)
+          NoCyclicBonds++;
   delete (BackEdgeStack);
   return NoCyclicBonds;
@@ -461 +495 @@
 void DepthFirstSearchAnalysis_Init(struct DFSAccounting &DFS, const molecule * const mol)
 {
-  DFS.AtomStack = new StackClass<atom *> (mol->AtomCount);
+  DFS.AtomStack = new StackClass<atom *> (mol->getAtomCount());
   DFS.CurrentGraphNr = 0;
   DFS.ComponentNumber = 0;
@@ -502 +536 @@
   bond *Binder = NULL;
 
-  if (AtomCount == 0)
+  if (getAtomCount() == 0)
     return SubGraphs;
   DoLog(0) && (Log() << Verbose(0) << "Begin of DepthFirstSearchAnalysis" << endl);
   DepthFirstSearchAnalysis_Init(DFS, this);
 
-  DFS.Root = start->next;
-  while (DFS.Root != end) { // if there any atoms at all
+  for (molecule::const_iterator iter = begin(); iter != end();) {
+    DFS.Root = *iter;
     // (1) mark all edges unused, empty stack, set atom->GraphNr = -1 for all
     DFS.AtomStack->ClearStack();
@@ -548 +582 @@
 
     // step on to next root
-    while ((DFS.Root != end) && (DFS.Root->GraphNr != -1)) {
-      //Log() << Verbose(1) << "Current next subgraph root candidate is " << Root->Name << "." << endl;
-      if (DFS.Root->GraphNr != -1) // if already discovered, step on
-        DFS.Root = DFS.Root->next;
+    while ((iter != end()) && ((*iter)->GraphNr != -1)) {
+      //Log() << Verbose(1) << "Current next subgraph root candidate is " << (*iter)->Name << "." << endl;
+      if ((*iter)->GraphNr != -1) // if already discovered, step on
+        iter++;
     }
   }
@@ -573 +607 @@
 {
   NoCyclicBonds = 0;
-  bond *Binder = first;
-  while (Binder->next != last) {
-    Binder = Binder->next;
-    if (Binder->rightatom->LowpointNr == Binder->leftatom->LowpointNr) { // cyclic ??
-      Binder->Cyclic = true;
-      NoCyclicBonds++;
-    }
-  }
+  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+      if ((*BondRunner)->leftatom == *AtomRunner)
+        if ((*BondRunner)->rightatom->LowpointNr == (*BondRunner)->leftatom->LowpointNr) { // cyclic ??
+          (*BondRunner)->Cyclic = true;
+          NoCyclicBonds++;
+        }
 }
 ;
@@ -599 +632 @@
 void molecule::OutputGraphInfoPerBond() const
 {
+  bond *Binder = NULL;
   DoLog(1) && (Log() << Verbose(1) << "Final graph info for each bond is:" << endl);
-  bond *Binder = first;
-  while (Binder->next != last) {
-    Binder = Binder->next;
-    DoLog(2) && (Log() << Verbose(2) << ((Binder->Type == TreeEdge) ? "TreeEdge " : "BackEdge ") << *Binder << ": <");
-    DoLog(0) && (Log() << Verbose(0) << ((Binder->leftatom->SeparationVertex) ? "SP," : "") << "L" << Binder->leftatom->LowpointNr << " G" << Binder->leftatom->GraphNr << " Comp.");
-    Binder->leftatom->OutputComponentNumber();
-    DoLog(0) && (Log() << Verbose(0) << " ===  ");
-    DoLog(0) && (Log() << Verbose(0) << ((Binder->rightatom->SeparationVertex) ? "SP," : "") << "L" << Binder->rightatom->LowpointNr << " G" << Binder->rightatom->GraphNr << " Comp.");
-    Binder->rightatom->OutputComponentNumber();
-    DoLog(0) && (Log() << Verbose(0) << ">." << endl);
-    if (Binder->Cyclic) // cyclic ??
-      DoLog(3) && (Log() << Verbose(3) << "Lowpoint at each side are equal: CYCLIC!" << endl);
-  }
+  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+      if ((*BondRunner)->leftatom == *AtomRunner) {
+        Binder = *BondRunner;
+        DoLog(2) && (Log() << Verbose(2) << ((Binder->Type == TreeEdge) ? "TreeEdge " : "BackEdge ") << *Binder << ": <");
+        DoLog(0) && (Log() << Verbose(0) << ((Binder->leftatom->SeparationVertex) ? "SP," : "") << "L" << Binder->leftatom->LowpointNr << " G" << Binder->leftatom->GraphNr << " Comp.");
+        Binder->leftatom->OutputComponentNumber();
+        DoLog(0) && (Log() << Verbose(0) << " ===  ");
+        DoLog(0) && (Log() << Verbose(0) << ((Binder->rightatom->SeparationVertex) ? "SP," : "") << "L" << Binder->rightatom->LowpointNr << " G" << Binder->rightatom->GraphNr << " Comp.");
+        Binder->rightatom->OutputComponentNumber();
+        DoLog(0) && (Log() << Verbose(0) << ">." << endl);
+        if (Binder->Cyclic) // cyclic ??
+          DoLog(3) && (Log() << Verbose(3) << "Lowpoint at each side are equal: CYCLIC!" << endl);
+      }
 }
 ;
@@ -624 +659 @@
 {
   BFS.AtomCount = AtomCount;
-  BFS.PredecessorList = Calloc<atom*> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: **PredecessorList");
-  BFS.ShortestPathList = Malloc<int> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ShortestPathList");
-  BFS.ColorList = Calloc<enum Shading> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ColorList");
+  BFS.PredecessorList = new atom*[AtomCount];
+  BFS.ShortestPathList = new int[AtomCount];
+  BFS.ColorList = new enum Shading[AtomCount];
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
 
-  for (int i = AtomCount; i--;)
+  for (int i = AtomCount; i--;) {
     BFS.ShortestPathList[i] = -1;
+    BFS.PredecessorList[i] = 0;
+  }
 };
 
@@ -639 +676 @@
 void FinalizeBFSAccounting(struct BFSAccounting &BFS)
 {
-  Free(&BFS.PredecessorList);
-  Free(&BFS.ShortestPathList);
-  Free(&BFS.ColorList);
+  delete[](BFS.PredecessorList);
+  delete[](BFS.ShortestPathList);
+  delete[](BFS.ColorList);
   delete (BFS.BFSStack);
   BFS.AtomCount = 0;
@@ -854 +891 @@
   if (MinRingSize != -1) { // if rings are present
     // go over all atoms
-    Root = mol->start;
-    while (Root->next != mol->end) {
-      Root = Root->next;
-
-      if (MinimumRingSize[Root->GetTrueFather()->nr] == mol->AtomCount) { // check whether MinimumRingSize is set, if not BFS to next where it is
+    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+      Root = *iter;
+
+      if (MinimumRingSize[Root->GetTrueFather()->nr] == mol->getAtomCount()) { // check whether MinimumRingSize is set, if not BFS to next where it is
         Walker = Root;
 
         //Log() << Verbose(1) << "---------------------------------------------------------------------------------------------------------" << endl;
-        CyclicStructureAnalysis_BFSToNextCycle(Root, Walker, MinimumRingSize, mol->AtomCount);
+        CyclicStructureAnalysis_BFSToNextCycle(Root, Walker, MinimumRingSize, mol->getAtomCount());
 
       }
@@ -892 +928 @@
   int MinRingSize = -1;
 
-  InitializeBFSAccounting(BFS, AtomCount);
+  InitializeBFSAccounting(BFS, getAtomCount());
 
   //Log() << Verbose(1) << "Back edge list - ";
@@ -966 +1002 @@
 void molecule::ResetAllBondsToUnused() const
 {
-  bond *Binder = first;
-  while (Binder->next != last) {
-    Binder = Binder->next;
-    Binder->ResetUsed();
-  }
+  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+      if ((*BondRunner)->leftatom == *AtomRunner)
+        (*BondRunner)->ResetUsed();
 }
 ;
@@ -1004 +1039 @@
     line << filename;
   AdjacencyFile.open(line.str().c_str(), ios::out);
-  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... ");
+  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
   if (AdjacencyFile != NULL) {
     AdjacencyFile << "m\tn" << endl;
     ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
     AdjacencyFile.close();
-    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line.str() << "." << endl);
     status = false;
   }
@@ -1036 +1071 @@
     line << filename;
   BondFile.open(line.str().c_str(), ios::out);
-  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... ");
+  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
   if (BondFile != NULL) {
     BondFile << "m\tn" << endl;
     ActOnAllAtoms(&atom::OutputBonds, &BondFile);
     BondFile.close();
-    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line.str() << "." << endl);
     status = false;
   }
@@ -1056 +1091 @@
   filename << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
   File.open(filename.str().c_str(), ios::out);
-  DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... ");
+  DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl);
   if (File == NULL)
     return false;
 
   // allocate storage structure
-  CurrentBonds = Calloc<int> (8, "molecule::CheckAdjacencyFileAgainstMolecule - CurrentBonds"); // contains parsed bonds of current atom
+  CurrentBonds = new int[8]; // contains parsed bonds of current atom
+  for(int i=0;i<8;i++)
+    CurrentBonds[i] = 0;
   return true;
 }
@@ -1070 +1107 @@
   File.close();
   File.clear();
-  Free(&CurrentBonds);
+  delete[](CurrentBonds);
 }
 ;
@@ -1090 +1127 @@
         NonMatchNumber++;
         status = false;
+        DoeLog(2) && (eLog() << Verbose(2) << id << " can not be found in list." << endl);
+      } else {
         //Log() << Verbose(0) << "[" << id << "]\t";
-      } else {
-        //Log() << Verbose(0) << id << "\t";
       }
     }
@@ -1114 +1151 @@
   bool status = true;
   atom *Walker = NULL;
-  char *buffer = NULL;
   int *CurrentBonds = NULL;
   int NonMatchNumber = 0; // will number of atoms with differing bond structure
   size_t CurrentBondsOfAtom = -1;
+  const int AtomCount = getAtomCount();
 
   if (!CheckAdjacencyFileAgainstMolecule_Init(path, File, CurrentBonds)) {
@@ -1124 +1161 @@
   }
 
-  buffer = Malloc<char> (MAXSTRINGSIZE, "molecule::CheckAdjacencyFileAgainstMolecule: *buffer");
+  char buffer[MAXSTRINGSIZE];
   // Parse the file line by line and count the bonds
   while (!File.eof()) {
@@ -1140 +1177 @@
       // compare against present bonds
       CheckAdjacencyFileAgainstMolecule_CompareBonds(status, NonMatchNumber, Walker, CurrentBondsOfAtom, AtomNr, CurrentBonds, ListOfAtoms);
-    }
-  }
-  Free(&buffer);
+    } else {
+      if (AtomNr != -1)
+        DoeLog(2) && (eLog() << Verbose(2) << AtomNr << " is not valid in the range of ids [" << 0 << "," << AtomCount << ")." << endl);
+    }
+  }
   CheckAdjacencyFileAgainstMolecule_Finalize(File, CurrentBonds);
 
@@ -1196 +1235 @@
   BFS.AtomCount = AtomCount;
   BFS.BondOrder = BondOrder;
-  BFS.PredecessorList = Calloc<atom*> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: **PredecessorList");
-  BFS.ShortestPathList = Calloc<int> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ShortestPathList");
-  BFS.ColorList = Malloc<enum Shading> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ColorList");
+  BFS.PredecessorList = new atom*[AtomCount];
+  BFS.ShortestPathList = new int[AtomCount];
+  BFS.ColorList = new enum Shading[AtomCount];
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
 
@@ -1207 +1246 @@
   // initialise each vertex as white with no predecessor, empty queue, color Root lightgray
   for (int i = AtomCount; i--;) {
+    BFS.PredecessorList[i] = NULL;
     BFS.ShortestPathList[i] = -1;
     if ((AddedAtomList != NULL) && (AddedAtomList[i] != NULL)) // mark already present atoms (i.e. Root and maybe others) as visited
@@ -1213 +1253 @@
       BFS.ColorList[i] = white;
   }
-  //BFS.ShortestPathList[Root->nr] = 0; //is set due to Calloc()
+  //BFS.ShortestPathList[Root->nr] = 0; // done by Calloc
 }
 ;
@@ -1219 +1259 @@
 void BreadthFirstSearchAdd_Free(struct BFSAccounting &BFS)
 {
-  Free(&BFS.PredecessorList);
-  Free(&BFS.ShortestPathList);
-  Free(&BFS.ColorList);
+  delete[](BFS.PredecessorList);
+  delete[](BFS.ShortestPathList);
+  delete[](BFS.ColorList);
   delete (BFS.BFSStack);
   BFS.AtomCount = 0;
@@ -1313 +1353 @@
     AddedAtomList[Root->nr] = Mol->AddCopyAtom(Root);
 
-  BreadthFirstSearchAdd_Init(BFS, Root, BondOrder, AtomCount, AddedAtomList);
+  BreadthFirstSearchAdd_Init(BFS, Root, BondOrder, getAtomCount(), AddedAtomList);
 
   // and go on ... Queue always contains all lightgray vertices
@@ -1360 +1400 @@
 {
   // reset parent list
-  ParentList = Calloc<atom*> (AtomCount, "molecule::BuildInducedSubgraph_Init: **ParentList");
+  ParentList = new atom*[AtomCount];
+  for (int i=0;i<AtomCount;i++)
+    ParentList[i] = NULL;
   DoLog(3) && (Log() << Verbose(3) << "Resetting ParentList." << endl);
 }
@@ -1369 +1411 @@
   // fill parent list with sons
   DoLog(3) && (Log() << Verbose(3) << "Filling Parent List." << endl);
-  atom *Walker = mol->start;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    ParentList[Walker->father->nr] = Walker;
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    ParentList[(*iter)->father->nr] = (*iter);
     // Outputting List for debugging
-    DoLog(4) && (Log() << Verbose(4) << "Son[" << Walker->father->nr << "] of " << Walker->father << " is " << ParentList[Walker->father->nr] << "." << endl);
-  }
-
-}
-;
+    DoLog(4) && (Log() << Verbose(4) << "Son[" << (*iter)->father->nr << "] of " << (*iter)->father << " is " << ParentList[(*iter)->father->nr] << "." << endl);
+  }
+};
 
 void BuildInducedSubgraph_Finalize(atom **&ParentList)
 {
-  Free(&ParentList);
+  delete[](ParentList);
 }
 ;
@@ -1389 +1427 @@
 {
   bool status = true;
-  atom *Walker = NULL;
   atom *OtherAtom = NULL;
   // check each entry of parent list and if ok (one-to-and-onto matching) create bonds
   DoLog(3) && (Log() << Verbose(3) << "Creating bonds." << endl);
-  Walker = Father->start;
-  while (Walker->next != Father->end) {
-    Walker = Walker->next;
-    if (ParentList[Walker->nr] != NULL) {
-      if (ParentList[Walker->nr]->father != Walker) {
+  for (molecule::const_iterator iter = Father->begin(); iter != Father->end(); ++iter) {
+    if (ParentList[(*iter)->nr] != NULL) {
+      if (ParentList[(*iter)->nr]->father != (*iter)) {
         status = false;
       } else {
-        for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
-          OtherAtom = (*Runner)->GetOtherAtom(Walker);
+        for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
+          OtherAtom = (*Runner)->GetOtherAtom((*iter));
           if (ParentList[OtherAtom->nr] != NULL) { // if otheratom is also a father of an atom on this molecule, create the bond
-            DoLog(4) && (Log() << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[Walker->nr]->getName() << " and " << ParentList[OtherAtom->nr]->getName() << "." << endl);
-            mol->AddBond(ParentList[Walker->nr], ParentList[OtherAtom->nr], (*Runner)->BondDegree);
+            DoLog(4) && (Log() << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[(*iter)->nr]->getName() << " and " << ParentList[OtherAtom->nr]->getName() << "." << endl);
+            mol->AddBond(ParentList[(*iter)->nr], ParentList[OtherAtom->nr], (*Runner)->BondDegree);
           }
         }
@@ -1427 +1462 @@
   bool status = true;
   atom **ParentList = NULL;
-
   DoLog(2) && (Log() << Verbose(2) << "Begin of BuildInducedSubgraph." << endl);
-  BuildInducedSubgraph_Init(ParentList, Father->AtomCount);
+  BuildInducedSubgraph_Init(ParentList, Father->getAtomCount());
   BuildInducedSubgraph_FillParentList(this, Father, ParentList);
   status = BuildInducedSubgraph_CreateBondsFromParent(this, Father, ParentList);