Changes in src/molecule_graph.cpp [112b09:c27778]

File:

• src/molecule_graph.cpp (modified) (10 diffs)

src/molecule_graph.cpp

@@ -12 +12 @@
 #include "bondgraph.hpp"
 #include "config.hpp"
+#include "defs.hpp"
 #include "element.hpp"
 #include "helpers.hpp"
@@ -663 +664 @@
   BFS.ColorList = new enum Shading[AtomCount];
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
+  BFS.TouchedStack = new StackClass<atom *> (AtomCount);
 
   for (int i = AtomCount; i--;) {
     BFS.ShortestPathList[i] = -1;
     BFS.PredecessorList[i] = 0;
+    BFS.ColorList[i] = white;
   }
 };
@@ -680 +683 @@
   delete[](BFS.ColorList);
   delete (BFS.BFSStack);
+  delete (BFS.TouchedStack);
   BFS.AtomCount = 0;
 };
@@ -824 +828 @@
       MinRingSize = RingSize;
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "No ring containing " << *BFS.Root << " with length equal to or smaller than " << MinimumRingSize[Walker->GetTrueFather()->nr] << " found." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "No ring containing " << *BFS.Root << " with length equal to or smaller than " << MinimumRingSize[BFS.Root->GetTrueFather()->nr] << " found." << endl);
   }
 };
@@ -1024 +1028 @@
 /** Storing the bond structure of a molecule to file.
  * Simply stores Atom::nr and then the Atom::nr of all bond partners per line.
- * \param *path path to file
- * \param *filename name of file
+ * \param &filename name of file
+ * \param path path to file, defaults to empty
  * \return true - file written successfully, false - writing failed
  */
-bool molecule::StoreAdjacencyToFile(char *path, char *filename)
+bool molecule::StoreAdjacencyToFile(std::string &filename, std::string path)
 {
   ofstream AdjacencyFile;
-  stringstream line;
+  string line;
   bool status = true;
 
-  if (path != NULL)
-    line << path << "/" << filename;
+  if (path != "")
+    line = path + "/" + filename;
   else
-    line << filename;
-  AdjacencyFile.open(line.str().c_str(), ios::out);
+    line = filename;
+  AdjacencyFile.open(line.c_str(), ios::out);
   DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
-  if (AdjacencyFile != NULL) {
+  if (AdjacencyFile.good()) {
     AdjacencyFile << "m\tn" << endl;
     ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
@@ -1046 +1050 @@
     DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line.str() << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line << "." << endl);
     status = false;
   }
@@ -1056 +1060 @@
 /** Storing the bond structure of a molecule to file.
  * Simply stores Atom::nr and then the Atom::nr of all bond partners, one per line.
- * \param *path path to file
- * \param *filename name of file
+ * \param &filename name of file
+ * \param path path to file, defaults to empty
  * \return true - file written successfully, false - writing failed
  */
-bool molecule::StoreBondsToFile(char *path, char *filename)
+bool molecule::StoreBondsToFile(std::string &filename, std::string path)
 {
   ofstream BondFile;
-  stringstream line;
+  string line;
   bool status = true;
 
-  if (path != NULL)
-    line << path << "/" << filename;
+  if (path != "")
+    line = path + "/" + filename;
   else
-    line << filename;
-  BondFile.open(line.str().c_str(), ios::out);
+    line = filename;
+  BondFile.open(line.c_str(), ios::out);
   DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
-  if (BondFile != NULL) {
+  if (BondFile.good()) {
     BondFile << "m\tn" << endl;
     ActOnAllAtoms(&atom::OutputBonds, &BondFile);
@@ -1078 +1082 @@
     DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line.str() << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line << "." << endl);
     status = false;
   }
@@ -1086 +1090 @@
 ;
 
-bool CheckAdjacencyFileAgainstMolecule_Init(char *path, ifstream &File, int *&CurrentBonds)
-{
-  stringstream filename;
-  filename << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
-  File.open(filename.str().c_str(), ios::out);
+bool CheckAdjacencyFileAgainstMolecule_Init(std::string &path, ifstream &File, int *&CurrentBonds)
+{
+  string filename;
+  filename = path + ADJACENCYFILE;
+  File.open(filename.c_str(), ios::out);
   DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl);
-  if (File == NULL)
+  if (File.fail())
     return false;
 
@@ -1146 +1150 @@
  * \return true - structure is equal, false - not equivalence
  */
-bool molecule::CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms)
+bool molecule::CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms)
 {
   ifstream File;