Changes in src/molecule_graph.cpp [af2c424:e4afb4]

File:

• src/molecule_graph.cpp (modified) (11 diffs)

src/molecule_graph.cpp

@@ -220 +220 @@
 
     // output bonds for debugging (if bond chain list was correctly installed)
-    ActOnAllAtoms( &atom::OutputBondOfAtom );
+    for_each(atoms.begin(),atoms.end(),mem_fun(&atom::OutputBondOfAtom));
   } else
     DoLog(1) && (Log() << Verbose(1) << "AtomCount is " << getAtomCount() << ", thus no bonds, no connections!." << endl);
@@ -233 +233 @@
  * \return true - bonds present, false - no bonds
  */
-bool molecule::hasBondStructure()
-{
-  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+bool molecule::hasBondStructure() const
+{
+  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
     if (!(*AtomRunner)->ListOfBonds.empty())
       return true;
@@ -285 +285 @@
     do {
       OldNo = No;
-      No = SumPerAtom( &atom::CorrectBondDegree );
+      No=0;
+      BOOST_FOREACH(atom *atom,atoms){
+        No+=atom->CorrectBondDegree();
+      }
     } while (OldNo != No);
     DoLog(0) && (Log() << Verbose(0) << " done." << endl);
@@ -515 +518 @@
   DFS.BackStepping = false;
   mol->ResetAllBondsToUnused();
-  mol->SetAtomValueToValue(-1, &atom::GraphNr);
-  mol->ActOnAllAtoms(&atom::InitComponentNr);
   DFS.BackEdgeStack->ClearStack();
 }
@@ -531 +532 @@
 }
 ;
+
+void molecule::init_DFS(struct DFSAccounting &DFS) const{
+  DepthFirstSearchAnalysis_Init(DFS, this);
+  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::resetGraphNr));
+  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::InitComponentNr));
+}
 
 /** Performs a Depth-First search on this molecule.
@@ -554 +561 @@
     return SubGraphs;
   DoLog(0) && (Log() << Verbose(0) << "Begin of DepthFirstSearchAnalysis" << endl);
-  DepthFirstSearchAnalysis_Init(DFS, this);
+  init_DFS(DFS);
 
   for (molecule::const_iterator iter = begin(); iter != end();) {
@@ -638 +645 @@
 {
   DoLog(1) && (Log() << Verbose(1) << "Final graph info for each atom is:" << endl);
-  ActOnAllAtoms( &atom::OutputGraphInfo );
+  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::OutputGraphInfo));
 }
 ;
@@ -1049 +1056 @@
  * \return true - file written successfully, false - writing failed
  */
-bool molecule::StoreAdjacencyToFile(std::string &filename, std::string path)
+bool molecule::StoreAdjacencyToFile(std::string filename, std::string path)
 {
   ofstream AdjacencyFile;
@@ -1063 +1070 @@
   if (AdjacencyFile.good()) {
     AdjacencyFile << "m\tn" << endl;
-    ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
+    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputAdjacency),&AdjacencyFile));
     AdjacencyFile.close();
     DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
@@ -1081 +1088 @@
  * \return true - file written successfully, false - writing failed
  */
-bool molecule::StoreBondsToFile(std::string &filename, std::string path)
+bool molecule::StoreBondsToFile(std::string filename, std::string path)
 {
   ofstream BondFile;
@@ -1095 +1102 @@
   if (BondFile.good()) {
     BondFile << "m\tn" << endl;
-    ActOnAllAtoms(&atom::OutputBonds, &BondFile);
+    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputBonds),&BondFile));
     BondFile.close();
     DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);