Changeset 08b88b for molecuilder/src/molecule_graph.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/molecule_graph.cpp (modified) (3 diffs)

molecuilder/src/molecule_graph.cpp

@@ -114 +114 @@
   *out << Verbose(0) << "Begin of CreateAdjacencyList." << endl;
   // remove every bond from the list
-  if ((first->next != last) && (last->previous != first)) { // there are bonds present
-    cleanup(first, last);
+  bond *Binder = NULL;
+  while (last->previous != first) {
+    Binder = last->previous;
+    Binder->leftatom->UnregisterBond(Binder);
+    Binder->rightatom->UnregisterBond(Binder);
+    removewithoutcheck(Binder);
   }
 
   // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)
   CountAtoms(out);
-  *out << Verbose(1) << "AtomCount " << AtomCount << "." << endl;
+  *out << Verbose(1) << "AtomCount " << AtomCount << " and bonddistance is " << bonddistance << "." << endl;
 
   if ((AtomCount > 1) && (bonddistance > 1.)) {
+    *out << Verbose(2) << "Creating Linked Cell structure ... " << endl;
     LC = new LinkedCell(this, bonddistance);
 
     // create a list to map Tesselpoint::nr to atom *
+    *out << Verbose(2) << "Creating TesselPoint to atom map ... " << endl;
     AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
     Walker = start;
@@ -134 +140 @@
 
     // 3a. go through every cell
+    *out << Verbose(2) << "Celling ... " << endl;
     for (LC->n[0] = 0; LC->n[0] < LC->N[0]; LC->n[0]++)
       for (LC->n[1] = 0; LC->n[1] < LC->N[1]; LC->n[1]++)
@@ -175 +182 @@
 
     // correct bond degree by comparing valence and bond degree
+    *out << Verbose(2) << "Correcting bond degree ... " << endl;
     CorrectBondDegree(out);