Changeset c1b4a4 for molecuilder/src/bondgraph.cpp

Timestamp:

Nov 3, 2009, 4:34:31 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

a3ffb44

Parents:

08b88b

Message:

"not working parsed molecule into subgraph splitting"-BUG fixed, BugFinder branch can be closed.

• config::Load() - atoms were not in the right order for MaxOrder-test (12). Hence, the BondFragmentAdjacency could not be parsed. Now, we just take the subgraphs as the association of each atom to a molecule, i.e. we make a list and then re-link each atom to its new connected subgraph molecule, which is returned as the MoleculeListClass.

other fixes:

• BondGraph::SetMaxDistanceToMaxOfCovalentRadii() - parses the molecule and set to max of covalent radii of elements found therein
• BondGraph::ConstructBondGraph() - SetMaxDistanceToMaxOfCovalentRadii() called before CreateAdjacencyList() to have current max_distance
• BUGFIX: molecule::CreateAdjacencyList() - BondCount was not set to zero after cleaning of list
• FIX: CreateFatherLookupTable() - as we use Calloc(), initialization to NULL was unnecessary

File:

• molecuilder/src/bondgraph.cpp (modified) (2 diffs)

molecuilder/src/bondgraph.cpp

@@ -84 +84 @@
     return false;
 
-  if (BondLengthMatrix == NULL) // no bond length matrix parsed?
+  if (BondLengthMatrix == NULL) { // no bond length matrix parsed?
+    SetMaxDistanceToMaxOfCovalentRadii(out, mol);
     mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::CovalentMinMaxDistance, this);
-  else
+  } else
     mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::BondLengthMatrixMinMaxDistance, this);
 
@@ -105 +106 @@
 };
 
-/** Determines the maximum of all element::CovalentRadius.
+/** Determines the maximum of all element::CovalentRadius for elements present in \a *mol.
  * \param *out output stream for debugging
- * \param *periode periodentafel with all elements.
+ * \param *mol molecule with all atoms and their respective elements.
  */
-double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const periodentafel * const periode)
+double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const molecule * const mol)
 {
   max_distance = 0.;
 
-  element * Runner = periode->start;
-  while (Runner->next != periode->end) {
+  atom *Runner = mol->start;
+  while (Runner->next != mol->end) {
     Runner = Runner->next;
-    if (Runner->CovalentRadius > max_distance)
-      max_distance = Runner->CovalentRadius;
+    if (Runner->type->CovalentRadius > max_distance)
+      max_distance = Runner->type->CovalentRadius;
   }
   max_distance *= 2.;