Changeset 08b88b for molecuilder/src/config.cpp

Timestamp:

Nov 3, 2009, 2:34:02 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

c1b4a4

Parents:

5f9f8b

git-author:

Frederik Heber <heber@…> (11/03/09 14:27:15)

git-committer:

Frederik Heber <heber@…> (11/03/09 14:34:02)

Message:

Fixing not created adjacency list, partially fixing subgraph dissection in config::Load()

• CreateAdjacencyList() was called with zero bonddistance.
• this was due to max_distance not being initialised in the constructor to 0 and subsequently not set if Bond Length Table was not found.
• new function SetMaxDistanceToMaxOfCovalentRadii() which sets the max_distance to twice the max of covalent radii of all elements.
• config::Load() - atoms in copied molecule (by DepthFirstSearchAnalysis()) are made their own father (and originals are removed).

File:

• molecuilder/src/config.cpp (modified) (1 diff)

molecuilder/src/config.cpp

@@ -1051 +1051 @@
   } else {
     cout << Verbose(0) << "Bond length table loading failed." << endl;
+    BG->SetMaxDistanceToMaxOfCovalentRadii((ofstream *)&cout, periode);
   }
 
   // 3. parse the molecule in
   LoadMolecule(mol, FileBuffer, periode, FastParsing);
-  mol->ActiveFlag = true;
-  MolList->insert(mol);
+  //mol->ActiveFlag = true;
+  //MolList->insert(mol);
 
   // 4. dissect the molecule into connected subgraphs
   BG->ConstructBondGraph((ofstream *)&cout, mol);
+
+  // 5. scan for connected subgraphs
+  MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
+  class StackClass<bond *> *BackEdgeStack = NULL;
+  Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, BackEdgeStack);
+  delete(BackEdgeStack);
+
+  // 6. dissect
+  atom ***ListOfLocalAtoms = NULL;
+  int FragmentCounter = 0;
+  MoleculeLeafClass *MolecularWalker = Subgraphs;
+  atom *Walker = NULL;
+  while (MolecularWalker->next != NULL) {
+    MolecularWalker = MolecularWalker->next;
+    // fill the bond structure of the individually stored subgraphs (goes through whole chained list by itself)
+    MolecularWalker->FillBondStructureFromReference((ofstream *)&cout, mol, FragmentCounter, ListOfLocalAtoms, false);  // we don't want to keep the created ListOfLocalAtoms
+    FragmentCounter++;
+    MolecularWalker->Leaf->ActiveFlag = true;
+    Walker = MolecularWalker->Leaf->start;
+    while (Walker->next != MolecularWalker->Leaf->end) {
+      Walker = Walker->next;
+      Walker->father = Walker;
+    }
+    MolList->insert(MolecularWalker->Leaf);
+    MolecularWalker->Leaf = NULL; // don't remove molecule when deleting MolecularWalker
+    delete(MolecularWalker->previous);
+  }
+  delete(MolecularWalker);
+  for (int i=0;i<FragmentCounter;i++)
+    Free(&ListOfLocalAtoms[i]);
+  Free(&ListOfLocalAtoms);
+  cout << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl;
+
+  // 6. free parsed in molecule
+  delete(mol);
 
   delete(FileBuffer);