Changes in src/molecule_graph.cpp [68f03d:920c70]

File:

• src/molecule_graph.cpp (modified) (17 diffs)

src/molecule_graph.cpp

@@ -12 +12 @@
 #include "element.hpp"
 #include "helpers.hpp"
+#include "info.hpp"
 #include "linkedcell.hpp"
 #include "lists.hpp"
@@ -54 +55 @@
 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");
+  // 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);
@@ -137 +143 @@
     // 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");
+    AtomMap = new atom *[AtomCount];
+    for (int i=0;i<AtomCount;i++)
+      AtomMap[i] = NULL;
     Walker = start;
     while (Walker->next != end) {
@@ -188 +196 @@
           }
         }
-    Free(&AtomMap);
+    delete[](AtomMap);
     delete (LC);
     DoLog(1) && (Log() << Verbose(1) << "I detected " << BondCount << " bonds in the molecule with distance " << BondDistance << "." << endl);
@@ -624 +632 @@
 {
   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 +649 @@
 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;
@@ -1061 +1071 @@
 
   // 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 +1082 @@
   File.close();
   File.clear();
-  Free(&CurrentBonds);
+  delete[](CurrentBonds);
 }
 ;
@@ -1114 +1126 @@
   bool status = true;
   atom *Walker = NULL;
-  char *buffer = NULL;
   int *CurrentBonds = NULL;
   int NonMatchNumber = 0; // will number of atoms with differing bond structure
@@ -1124 +1135 @@
   }
 
-  buffer = Malloc<char> (MAXSTRINGSIZE, "molecule::CheckAdjacencyFileAgainstMolecule: *buffer");
+  char buffer[MAXSTRINGSIZE];
   // Parse the file line by line and count the bonds
   while (!File.eof()) {
@@ -1142 +1153 @@
     }
   }
-  Free(&buffer);
   CheckAdjacencyFileAgainstMolecule_Finalize(File, CurrentBonds);
 
@@ -1196 +1206 @@
   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 +1217 @@
   // 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 +1224 @@
       BFS.ColorList[i] = white;
   }
-  //BFS.ShortestPathList[Root->nr] = 0; //is set due to Calloc()
+  //BFS.ShortestPathList[Root->nr] = 0; // done by Calloc
 }
 ;
@@ -1219 +1230 @@
 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;
@@ -1360 +1371 @@
 {
   // 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);
 }
@@ -1382 +1395 @@
 void BuildInducedSubgraph_Finalize(atom **&ParentList)
 {
-  Free(&ParentList);
+  delete[](ParentList);
 }
 ;