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DFS does not copy atoms or molecules anymore but reinitiates the current molecule structure with present atoms, used new class ConnectedSubgraph for that. New functions:
- UpdateMoleculeStructure() - reinstantiates molecules.
- getMoleculeStructure() - puts molecules into chained list.
adapted because of that:
- DepthFirstSearchAction: uses DFS and CSA functors, also UpdateMoleculeStructure() such that CSA has current structure.
- FragmentationAction: assumes connectivity fully present, DFS created.
- SubgraphDissectionAction: uses DFS and UpdateMoleculeStructure().
- molecule::FragmentMolecule(): no more DFS, instead DFS has to happen beforehand and is given as parameter, used to obtain chained list for compatibility for the moment.
DepthFirstSearchAnalysis::SetNextComponentNumber() bugfix due to wrong assert.

TESTFIXES:

Fragmentation and regression test Fragmentation/FragmentMolecule: FragmentationAction now needs SubgraphDissectionAction beforehand.
shifted id (down by one) due to non-copying (before: one big molecule, copied and split up system started at 1, now it starts at 0):
- (Un)Selection/Atoms/AllAtomsOfMolecule
- Analysis/SurfaceCorrelation
- (Un)Selection/Molecules/MoleculeById (also renamed post-files accordingly)
- (Un)Selection/Molecules/MoleculeByName

File:

: 1 edited

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (3 diffs)

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: Unmodified
: Added
: Removed

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

-              r1a4d4fe
+              r49c059
 #include "CodePatterns/Verbose.hpp"
 #include "Graph/BondGraph.hpp"
+#include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
 …
   // 2. scan for connected subgraphs
+  LOG(0, "STATUS: Analysing adjacency graph.");
+  MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
+  std::deque<bond *> *BackEdgeStack = NULL;
+  Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
+  delete(BackEdgeStack);
+  if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
+  DepthFirstSearchAnalysis DFS;
+  DFS();
+  DFS.UpdateMoleculeStructure();
+  if (!World::getInstance().numMolecules()) {
     //World::getInstance().destroyMolecule(mol);
     DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms." << endl);
 …
+  }
+  //int FragmentCounter = Subgraphs->next->Count();
+  // TODO: When DepthFirstSearchAnalysis does not use AddCopyAtom() anymore, we don't need to delete all original atoms
+  LOG(0, "STATUS: Creating molecules as connected subgraphs.");
+  {
+    {
+      atom **ListOfAtoms = NULL;
+      // 3a. re-create bond structure and insert molecules into general MoleculeListClass
+      MoleculeLeafClass *MoleculeWalker = Subgraphs->next;
+      while (MoleculeWalker->next != NULL) {
+        ListOfAtoms = NULL;
+        MoleculeWalker->Leaf->FillBondStructureFromReference(mol, ListOfAtoms, true);  // we want to keep the created ListOfLocalAtoms
+        molecules->insert(MoleculeWalker->Leaf);
+        MoleculeWalker = MoleculeWalker->next;
+      }
+      molecules->insert(MoleculeWalker->Leaf);
+      ListOfAtoms = NULL;
+      MoleculeWalker->Leaf->FillBondStructureFromReference(mol, ListOfAtoms, true);  // we want to keep the created ListOfLocalAtoms
+    }
+    // 3b. store map from new to old ids for 3d
+    vector <atom *> allatoms = World::getInstance().getAllAtoms();
+    AtomAtomList newtooldlist;
+    for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner)
+      if ((*AtomRunner)->father != (*AtomRunner))
+        newtooldlist.insert( std::pair<atomId_t, atomId_t> ((*AtomRunner)->getId(),(*AtomRunner)->father->getId()) );
+    {
+      // 3c. destroy the original molecule
+      for (molecule::iterator AtomRunner = mol->begin(); !mol->empty(); AtomRunner = mol->begin())
+        World::getInstance().destroyAtom(*AtomRunner);
+      World::getInstance().destroyMolecule(mol);
+    }
+    {
+      // 3d. convert to old Ids and correct fathers (AddCopyAtom sets father to original atom, which has been destroyed).
+      vector <atom *> allatoms = World::getInstance().getAllAtoms();
+      for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
+        World::getInstance().changeAtomId((*AtomRunner)->getId(), newtooldlist[(*AtomRunner)->getId()]);
+        (*AtomRunner)->father = *AtomRunner;
+      }
+    }
+  }
+  // 4. free Leafs
+  LOG(0, "STATUS: Done.");
+  MoleculeLeafClass *MolecularWalker = Subgraphs;
+  while (MolecularWalker->next != NULL) {
+    MolecularWalker->Leaf = NULL;
+    MolecularWalker = MolecularWalker->next;
+    delete(MolecularWalker->previous);
+  }
+  MolecularWalker->Leaf = NULL;
+  delete(MolecularWalker);
+  DoLog(1) && (Log() << Verbose(1) << "I scanned " << molecules->ListOfMolecules.size() << " molecules." << endl);
+  DoLog(1) && (Log() << Verbose(1) << "I scanned " << World::getInstance().numMolecules() << " molecules." << endl);
   return Action::state_ptr(UndoState);

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Changeset 49c059 for src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

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src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

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