Changeset 08b88b for molecuilder/src/moleculelist.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/moleculelist.cpp (modified) (4 diffs)

molecuilder/src/moleculelist.cpp

@@ -12 +12 @@
 #include "helpers.hpp"
 #include "linkedcell.hpp"
+#include "lists.hpp"
 #include "molecule.hpp"
 #include "memoryallocator.hpp"
@@ -829 +830 @@
 
   if (status) {
-    *out << Verbose(1) << "Creating adjacency list for subgraph " << this
-        << "." << endl;
+    *out << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl;
+    // remove every bond from the list
+    bond *Binder = NULL;
+    while (Leaf->last->previous != Leaf->first) {
+      Binder = Leaf->last->previous;
+      Binder->leftatom->UnregisterBond(Binder);
+      Binder->rightatom->UnregisterBond(Binder);
+      removewithoutcheck(Binder);
+    }
+
     Walker = Leaf->start;
     while (Walker->next != Leaf->end) {
@@ -847 +856 @@
       }
     }
-//    FragmentCounter++;
-//    if (next != NULL)
-//      status = next->FillBondStructureFromReference(out, reference, FragmentCounter, ListOfLocalAtoms);
-//    FragmentCounter--;
   }
 
@@ -916 +921 @@
   bool status = true;
 
-  int Counter = Count();
   if (ListOfLocalAtoms == NULL) { // allocated initial pointer
     // allocate and set each field to NULL
+    const int Counter = Count();
     ListOfLocalAtoms = Calloc<atom**>(Counter, "MoleculeLeafClass::FillListOfLocalAtoms - ***ListOfLocalAtoms");
-    if (ListOfLocalAtoms != NULL) {
-      FreeList = FreeList && true;
-    } else
+    if (ListOfLocalAtoms == NULL) {
+      FreeList = FreeList && false;
       status = false;
+    }
   }