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

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"
@@ -55 +54 @@
 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;
-  char line[MAXSTRINGSIZE];
-
-  if (input->fail()) {
-    DoeLog(0) && (eLog() << Verbose(0) << "Opening of bond file failed \n");
-    performCriticalExit();
+
+  if (!input) {
+    DoLog(1) && (Log() << Verbose(1) << "Opening silica failed \n");
   };
 
-  // skip header
-  input->getline(line,MAXSTRINGSIZE);
-  DoLog(1) && (Log() << Verbose(1) << "Scanning file ... \n");
+  *input >> ws >> atom1;
+  *input >> ws >> atom2;
+  DoLog(1) && (Log() << Verbose(1) << "Scanning file\n");
   while (!input->eof()) // Check whether we read everything already
   {
-    input->getline(line,MAXSTRINGSIZE);
-    stringstream zeile(line);
-    zeile >> atom1;
-    zeile >> atom2;
-
-    DoLog(2) && (Log() << Verbose(2) << "Looking for atoms " << atom1 << " and " << atom2 << "." << endl);
+    *input >> ws >> atom1;
+    *input >> ws >> atom2;
+
     if (atom2 < atom1) //Sort indices of atoms in order
       flip(atom1, atom2);
@@ -143 +137 @@
     // create a list to map Tesselpoint::nr to atom *
     DoLog(2) && (Log() << Verbose(2) << "Creating TesselPoint to atom map ... " << endl);
-    AtomMap = new atom *[AtomCount];
-    for (int i=0;i<AtomCount;i++)
-      AtomMap[i] = NULL;
+    AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
     Walker = start;
     while (Walker->next != end) {
@@ -196 +188 @@
           }
         }
-    delete[](AtomMap);
+    Free(&AtomMap);
     delete (LC);
     DoLog(1) && (Log() << Verbose(1) << "I detected " << BondCount << " bonds in the molecule with distance " << BondDistance << "." << endl);
@@ -632 +624 @@
 {
   BFS.AtomCount = AtomCount;
-  BFS.PredecessorList = new atom*[AtomCount];
-  BFS.ShortestPathList = new int[AtomCount];
-  BFS.ColorList = new enum Shading[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.BFSStack = new StackClass<atom *> (AtomCount);
 
-  for (int i = AtomCount; i--;) {
+  for (int i = AtomCount; i--;)
     BFS.ShortestPathList[i] = -1;
-    BFS.PredecessorList[i] = 0;
-  }
 };
 
@@ -649 +639 @@
 void FinalizeBFSAccounting(struct BFSAccounting &BFS)
 {
-  delete[](BFS.PredecessorList);
-  delete[](BFS.ShortestPathList);
-  delete[](BFS.ColorList);
+  Free(&BFS.PredecessorList);
+  Free(&BFS.ShortestPathList);
+  Free(&BFS.ColorList);
   delete (BFS.BFSStack);
   BFS.AtomCount = 0;
@@ -1071 +1061 @@
 
   // allocate storage structure
-  CurrentBonds = new int[8]; // contains parsed bonds of current atom
-  for(int i=0;i<8;i++)
-    CurrentBonds[i] = 0;
+  CurrentBonds = Calloc<int> (8, "molecule::CheckAdjacencyFileAgainstMolecule - CurrentBonds"); // contains parsed bonds of current atom
   return true;
 }
@@ -1082 +1070 @@
   File.close();
   File.clear();
-  delete[](CurrentBonds);
+  Free(&CurrentBonds);
 }
 ;
@@ -1126 +1114 @@
   bool status = true;
   atom *Walker = NULL;
+  char *buffer = NULL;
   int *CurrentBonds = NULL;
   int NonMatchNumber = 0; // will number of atoms with differing bond structure
@@ -1135 +1124 @@
   }
 
-  char buffer[MAXSTRINGSIZE];
+  buffer = Malloc<char> (MAXSTRINGSIZE, "molecule::CheckAdjacencyFileAgainstMolecule: *buffer");
   // Parse the file line by line and count the bonds
   while (!File.eof()) {
@@ -1153 +1142 @@
     }
   }
+  Free(&buffer);
   CheckAdjacencyFileAgainstMolecule_Finalize(File, CurrentBonds);
 
@@ -1206 +1196 @@
   BFS.AtomCount = AtomCount;
   BFS.BondOrder = BondOrder;
-  BFS.PredecessorList = new atom*[AtomCount];
-  BFS.ShortestPathList = new int[AtomCount];
-  BFS.ColorList = new enum Shading[AtomCount];
+  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.BFSStack = new StackClass<atom *> (AtomCount);
 
@@ -1217 +1207 @@
   // 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
@@ -1224 +1213 @@
       BFS.ColorList[i] = white;
   }
-  //BFS.ShortestPathList[Root->nr] = 0; // done by Calloc
+  //BFS.ShortestPathList[Root->nr] = 0; //is set due to Calloc()
 }
 ;
@@ -1230 +1219 @@
 void BreadthFirstSearchAdd_Free(struct BFSAccounting &BFS)
 {
-  delete[](BFS.PredecessorList);
-  delete[](BFS.ShortestPathList);
-  delete[](BFS.ColorList);
+  Free(&BFS.PredecessorList);
+  Free(&BFS.ShortestPathList);
+  Free(&BFS.ColorList);
   delete (BFS.BFSStack);
   BFS.AtomCount = 0;
@@ -1371 +1360 @@
 {
   // reset parent list
-  ParentList = new atom*[AtomCount];
-  for (int i=0;i<AtomCount;i++)
-    ParentList[i] = NULL;
+  ParentList = Calloc<atom*> (AtomCount, "molecule::BuildInducedSubgraph_Init: **ParentList");
   DoLog(3) && (Log() << Verbose(3) << "Resetting ParentList." << endl);
 }
@@ -1395 +1382 @@
 void BuildInducedSubgraph_Finalize(atom **&ParentList)
 {
-  delete[](ParentList);
+  Free(&ParentList);
 }
 ;