Changeset d50d2a for molecuilder/src/molecules.cpp

Timestamp:

May 7, 2008, 1:38:13 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

a01955

Parents:

417bb5

Message:

AtomStackClass -> template <typename T> StackClass<T> change in new file stackclass.hpp, other templates to helpers.hpp

StackClass was changed to a template and as template code may only be present in header file was moved to a new
header file stackclass.hpp. New file was added to Makefile.am
Other templates (list management et al) were moved to helpers.hpp as they are more sensibly placed there.

File:

• molecuilder/src/molecules.cpp (modified) (13 diffs)

molecuilder/src/molecules.cpp ¶

@@ -1419 +1419 @@
 MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(ofstream *out, bool ReturnStack, int &MinimumRingSize)
 {
-  AtomStackClass *AtomStack = new AtomStackClass(AtomCount);
+  class StackClass<atom *> *AtomStack;
+  AtomStack = new StackClass<atom *>(AtomCount);
+  class StackClass<bond *> *BackEdgeStack = new StackClass<bond *> (BondCount);
   MoleculeLeafClass *SubGraphs = new MoleculeLeafClass(NULL);
   MoleculeLeafClass *LeafWalker = SubGraphs;
   int CurrentGraphNr = 0, OldGraphNr;
-  int CyclicBonds;
   int ComponentNumber = 0;
   atom *Walker = NULL, *OtherAtom = NULL, *Root = start->next;
@@ -1434 +1435 @@
   ResetAllAtomNumbers();
   InitComponentNumbers();
+  BackEdgeStack->ClearStack();
   while (Root != end) { // if there any atoms at all
     // (1) mark all edges unused, empty stack, set atom->GraphNr = 0 for all
@@ -1468 +1470 @@
             // (4a) ... if "other" atom has been visited (GraphNr != 0), set lowpoint to minimum of both, go to (3)
             Binder->Type = BackEdge;
+            BackEdgeStack->Push(Binder);
             Walker->LowpointNr = ( Walker->LowpointNr < OtherAtom->GraphNr ) ? Walker->LowpointNr : OtherAtom->GraphNr;
             *out << Verbose(3) << "(4a) Visited: Setting Lowpoint of Walker[" << Walker->Name << "] to " << Walker->LowpointNr << "." << endl;
@@ -1568 +1571 @@
   }
 
-  // correct cyclic bonds that are not included in "same LP" argument
-  Binder = first;
-  while (Binder->next != last) {
-    Binder = Binder->next;
-    Walker = Binder->leftatom;
-    OtherAtom = Binder->rightatom;
-    // now check whether both have a cyclic bond in their list
-    CyclicBonds = 0;   // counts cyclic bonds;
-    for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++)
-      if ((CyclicBonds == 0) && (ListOfBondsPerAtom[Walker->nr][i]->Cyclic))
-        CyclicBonds = 1;  
-    for(int i=0;i<NumberOfBondsPerAtom[OtherAtom->nr];i++)
-      if ((CyclicBonds == 1) && (ListOfBondsPerAtom[OtherAtom->nr][i]->Cyclic))
-        CyclicBonds = 2;  
-    Binder->Cyclic = (Binder->Cyclic) || (CyclicBonds == 2); // set the Cyclic criterium either or ... 
-  }
-  
-  // further analysis of the found cycles (print rings, get minimum cycle length)
+  // analysis of the cycles (print rings, get minimum cycle length)
   CyclicStructureAnalysis(out, MinimumRingSize);
+
   *out << Verbose(1) << "Final graph info for each atom is:" << endl;
   Walker = start;
@@ -1624 +1611 @@
 void molecule::CyclicStructureAnalysis(ofstream *out, int &MinimumRingSize)
 {
-  AtomStackClass *AtomStack = new AtomStackClass(AtomCount);
+  class StackClass<atom *> *AtomStack = new StackClass<atom *>(AtomCount);
   int LP;
   atom *Walker = NULL, *OtherAtom = NULL, *Root = NULL, *Runner = NULL;
@@ -1630 +1617 @@
   int RingSize, NumCycles;
 
-  // go through every atom
+  // count number of cyclic bonds per atom and push all with 3 cyclic bonds onto stack
   AtomStack->ClearStack();
   int *NoCyclicBondsPerAtom = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CyclicStructureAnalysis: *NoCyclicBondsPerAtom");
@@ -2065 +2052 @@
   line << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
   File.open(line.str().c_str(), ios::out);
-  *out << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl;
+  *out << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... ";
   if (File != NULL) {
     // allocate storage structure
@@ -2119 +2106 @@
     status = false;
   }
+  *out << endl;
   Free((void **)&buffer, "molecule::CheckAdjacencyFileAgainstMolecule: *buffer");
   
@@ -2620 +2608 @@
 
 /** Adds atoms up to \a BondCount distance from \a *Root and notes them down in \a **AddedAtomList.
- * Gray vertices are always enqueued in an AtomStackClass FIFO queue, the rest is usual BFS with adding vertices found was
+ * Gray vertices are always enqueued in an StackClass<atom *> FIFO queue, the rest is usual BFS with adding vertices found was
  * white and putting into queue. 
  * \param *out output stream for debugging
@@ -2636 +2624 @@
   int *ShortestPathList = (int *) Malloc(sizeof(int)*AtomCount, "molecule::BreadthFirstSearchAdd: *ShortestPathList");
   enum Shading *ColorList = (enum Shading *) Malloc(sizeof(enum Shading)*AtomCount, "molecule::BreadthFirstSearchAdd: *ColorList");
-  AtomStackClass *AtomStack = new AtomStackClass(AtomCount);
+  class StackClass<atom *> *AtomStack = new StackClass<atom *>(AtomCount);
   atom *Walker = NULL, *OtherAtom = NULL;
   bond *Binder = NULL;
@@ -2802 +2790 @@
 
 
-/** Looks through a AtomStackClass and returns the likeliest removal candiate.
+/** Looks through a StackClass<atom *> and returns the likeliest removal candiate.
  * \param *out output stream for debugging messages
  * \param *&Leaf KeySet to look through
@@ -2922 +2910 @@
   enum Shading *ColorVertexList = (enum Shading *) Malloc(sizeof(enum Shading)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *ColorList");
   enum Shading *ColorEdgeList = (enum Shading *) Malloc(sizeof(enum Shading)*BondCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *ColorBondList");
-  AtomStackClass *RootStack = new AtomStackClass(AtomCount);
-  AtomStackClass *TouchedStack = new AtomStackClass((int)pow(4,Order)+2); // number of atoms reached from one with maximal 4 bonds plus Root itself
-  AtomStackClass *SnakeStack = new AtomStackClass(Order+1); // equal to Order is not possible, as then the AtomStackClass cannot discern between full and empty stack!
+  StackClass<atom *> *RootStack = new StackClass<atom *>(AtomCount);
+  StackClass<atom *> *TouchedStack = new StackClass<atom *>((int)pow(4,Order)+2); // number of atoms reached from one with maximal 4 bonds plus Root itself
+  StackClass<atom *> *SnakeStack = new StackClass<atom *>(Order+1); // equal to Order is not possible, as then the StackClass<atom *> cannot discern between full and empty stack!
   MoleculeLeafClass *Leaflet = NULL, *TempLeaf = NULL; 
   MoleculeListClass *FragmentList = NULL;
@@ -3489 +3477 @@
   double tmp;
   vector TranslationVector;
-  //AtomStackClass *CompStack = NULL;
-  AtomStackClass *AtomStack = new AtomStackClass(AtomCount);
+  //class StackClass<atom *> *CompStack = NULL;
+  class StackClass<atom *> *AtomStack = new StackClass<atom *>(AtomCount);
   bool flag = true;