Changes in src/Actions/FragmentationAction/SubgraphDissectionAction.cpp [952f38:bcf653]

File:

• src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (5 diffs)

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp ¶

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /*
  * SubgraphDissectionAction.cpp
@@ -6 +13 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
 #include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "Actions/ActionRegistry.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
+#include "Descriptors/MoleculeDescriptor.hpp"
+
 #include "atom.hpp"
+#include "bond.hpp"
+#include "bondgraph.hpp"
 #include "config.hpp"
 #include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
 #include "molecule.hpp"
-#include "Descriptors/MoleculeDescriptor.hpp"
 #include "stackclass.hpp"
 #include "World.hpp"
@@ -27 +44 @@
 #include "Actions/ValueStorage.hpp"
 
+// memento to remember the state when undoing
+
+typedef std::map< moleculeId_t, std::vector<atomId_t> > MolAtomList;
+
+class FragmentationSubgraphDissectionState : public ActionState {
+public:
+  FragmentationSubgraphDissectionState(const MolAtomList &_moleculelist) :
+   moleculelist(_moleculelist)
+  {}
+  MolAtomList moleculelist;
+};
+
 const char FragmentationSubgraphDissectionAction::NAME[] = "subgraph-dissect";
 
@@ -36 +65 @@
 {}
 
+/** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
+ */
 void FragmentationSubgraphDissection() {
   ActionRegistry::getInstance().getActionByName(FragmentationSubgraphDissectionAction::NAME)->call(Action::NonInteractive);
@@ -51 +82 @@
 Action::state_ptr FragmentationSubgraphDissectionAction::performCall() {
   DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
-  // @TODO rather do the dissection afterwards
+
+  // first create undo state
+  MolAtomList moleculelist;
+  vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
+  for (vector<molecule *>::const_iterator moliter = allmolecules.begin(); moliter != allmolecules.end(); ++moliter) {
+    std::vector<atomId_t> atomlist;
+    atomlist.resize((*moliter)->size());
+    for (molecule::const_iterator atomiter = (*moliter)->begin(); atomiter != (*moliter)->end(); ++atomiter) {
+      atomlist.push_back((*atomiter)->getId());
+    }
+    moleculelist.insert( std::pair< moleculeId_t, std::vector<atomId_t> > ((*moliter)->getId(), atomlist));
+  }
+  FragmentationSubgraphDissectionState *UndoState = new FragmentationSubgraphDissectionState(moleculelist);
+
   MoleculeListClass *molecules = World::getInstance().getMolecules();
-  molecules->DissectMoleculeIntoConnectedSubgraphs(World::getInstance().getPeriode(), World::getInstance().getConfig());
-  return Action::success;
+  config * const configuration = World::getInstance().getConfig();
+
+  // 0a. remove all present molecules
+  for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
+    molecules->erase(*MolRunner);
+    World::getInstance().destroyMolecule(*MolRunner);
+  }
+
+  // 0b. remove all bonds and construct a molecule with all atoms
+  molecule *mol = World::getInstance().createMolecule();
+  {
+    vector <atom *> allatoms = World::getInstance().getAllAtoms();
+    for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
+      for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+        delete(*BondRunner);
+      mol->AddAtom(*AtomRunner);
+    }
+  }
+
+  // 1. create the bond structure of the single molecule
+  if (configuration->BG != NULL) {
+    if (!configuration->BG->ConstructBondGraph(mol)) {
+      World::getInstance().destroyMolecule(mol);
+      DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
+      return Action::failure;
+    }
+  } else {
+    DoeLog(1) && (eLog()<< Verbose(1) << "There is no BondGraph class present to create bonds." << endl);
+    return Action::failure;
+  }
+
+  // 2. scan for connected subgraphs
+  MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
+  class StackClass<bond *> *BackEdgeStack = NULL;
+  Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
+  delete(BackEdgeStack);
+  if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
+    //World::getInstance().destroyMolecule(mol);
+    DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms." << endl);
+    return Action::failure;
+  }
+  int FragmentCounter = Subgraphs->next->Count();
+
+  // TODO: When DepthFirstSearchAnalysis does not use AddCopyAtom() anymore, we don't need to delete all original atoms
+  {
+    // 3a. destroy the original molecule
+    for (molecule::iterator AtomRunner = mol->begin(); !mol->empty(); AtomRunner = mol->begin())
+      World::getInstance().destroyAtom(*AtomRunner);
+    World::getInstance().destroyMolecule(mol);
+    // 3b. 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) {
+      (*AtomRunner)->father = *AtomRunner;
+    }
+  }
+
+  // 4. free Leafs
+  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 " << FragmentCounter << " molecules." << endl);
+
+  return Action::state_ptr(UndoState);
 }
 
 Action::state_ptr FragmentationSubgraphDissectionAction::performUndo(Action::state_ptr _state) {
-//  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
-
-  return Action::failure;
-//  string newName = state->mol->getName();
-//  state->mol->setName(state->lastName);
-//
-//  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
+  FragmentationSubgraphDissectionState *state = assert_cast<FragmentationSubgraphDissectionState*>(_state.get());
+
+  {
+    // remove all present molecules
+    MoleculeListClass *molecules = World::getInstance().getMolecules();
+    vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
+    for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
+      molecules->erase(*MolRunner);
+      World::getInstance().destroyMolecule(*MolRunner);
+    }
+  }
+
+  {
+    // construct the old state
+    molecule *mol = NULL;
+    for (MolAtomList::const_iterator iter = state->moleculelist.begin(); iter != state->moleculelist.end(); ++iter) {
+      mol = World::getInstance().createMolecule();
+      if (mol->getId() != (*iter).first)
+        World::getInstance().changeMoleculeId(mol->getId(), (*iter).first);
+      for (std::vector<atomId_t>::const_iterator atomiter = (*iter).second.begin(); atomiter != (*iter).second.end(); ++atomiter)
+        mol->AddAtom(World::getInstance().getAtom(AtomById(*atomiter)));
+    }
+  }
+
+  return Action::state_ptr(_state);
 }
 
 Action::state_ptr FragmentationSubgraphDissectionAction::performRedo(Action::state_ptr _state){
-  return Action::failure;
+  return performCall();
 }
 
 bool FragmentationSubgraphDissectionAction::canUndo() {
-  return false;
+  return true;
 }
 
 bool FragmentationSubgraphDissectionAction::shouldUndo() {
-  return false;
+  return true;
 }