Changeset 478683 for molecuilder/src/moleculelist.cpp

Timestamp:

Jan 26, 2010, 12:52:31 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

8d0b25, d34341

Parents:

551a58

Message:

GetDistanceToSurface() separated, filling now with water instead of boron, DissectMoleculeIntoConnectedSubgraphs() now working on list of molecules instead of single one.

• MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() so far was working on a single molecule (given by parameter) instead of the list already contained in the list of its class.
• Tesselation::GetDistanceSquaredToSurface() is split up into function of same name, which calls finds the closest triangle and calls Tesselation::GetDistanceSquaredToTriangle() which contains the former code.
• PeriodicCorrelationToSurface() was adapted to the above split.
• in tesselation.cpp lots of list<> and set<>s were replaced by the already present and appropriate define's.

• small verbosity changes in: MatrixContainer::ParseMatrix(), TesselPoint::TesselPoint(), TesselPoint::~TesselPoint(), PointCloud::PointCloud(), PointCloud::~PointCloud(), Tesselation::GuessStartingTriangle(), BondGraph::LoadBondLengthTable() (status of parsing gives appropriate message).

Signed-off-by: Frederik Heber <heber@…>

File:

• molecuilder/src/moleculelist.cpp (modified) (3 diffs)

molecuilder/src/moleculelist.cpp

@@ -741 +741 @@
 /** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
  * \param *out output stream for debugging
- * \param *mol molecule with atoms to dissect
+ * \param *periode periodentafel
  * \param *configuration config with BondGraph
  */
-void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration)
-{
+void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
+{
+  molecule *mol = new molecule(periode);
+  atom *Walker = NULL;
+  atom *Advancer = NULL;
+  bond *Binder = NULL;
+  bond *Stepper = NULL;
+  // 0. gather all atoms into single molecule
+  for (MoleculeList::iterator MolRunner = ListOfMolecules.begin(); !ListOfMolecules.empty(); MolRunner = ListOfMolecules.begin()) {
+    // shift all atoms to new molecule
+    Advancer = (*MolRunner)->start->next;
+    while (Advancer != (*MolRunner)->end) {
+      Walker = Advancer;
+      Advancer = Advancer->next;
+      Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
+      unlink(Walker);
+      Walker->father = Walker;
+      mol->AddAtom(Walker);    // counting starts at 1
+    }
+    // remove all bonds
+    Stepper = (*MolRunner)->first->next;
+    while (Stepper != (*MolRunner)->last) {
+      Binder = Stepper;
+      Stepper = Stepper->next;
+      delete(Binder);
+    }
+    // remove the molecule
+    delete(*MolRunner);
+    ListOfMolecules.erase(MolRunner);
+  }
+
   // 1. dissect the molecule into connected subgraphs
   configuration->BG->ConstructBondGraph(mol);
@@ -779 +808 @@
   int *MolMap = Calloc<int>(mol->AtomCount, "config::Load() - *MolMap");
   MoleculeLeafClass *MolecularWalker = Subgraphs;
-  atom *Walker = NULL;
+  Walker = NULL;
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
@@ -809 +838 @@
   }
   // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
-  bond *Binder = mol->first;
+  Binder = mol->first;
   while (mol->first->next != mol->last) {
     Binder = mol->first->next;