Changeset 6c438f for src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

Timestamp:

Aug 28, 2010, 3:21:11 AM (15 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

a6e6b5, f8982c

Parents:

2ad482 (diff), fd4905 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (08/28/10 03:17:48)

git-committer:

Frederik Heber <heber@…> (08/28/10 03:21:11)

Message:

Merge branch 'StructureRefactoring' into Shapes

Conflicts:

src/Box.cpp
src/Box.hpp
src/Descriptors/AtomShapeDescriptor.cpp
src/Descriptors/AtomShapeDescriptor.hpp
src/Descriptors/AtomShapeDescriptor_impl.hpp
src/LinearAlgebra/Line.cpp
src/LinearAlgebra/Line.hpp
src/LinearAlgebra/Matrix.cpp
src/LinearAlgebra/Matrix.hpp
src/Makefile.am
src/Shapes/BaseShapes.cpp
src/Shapes/BaseShapes_impl.hpp
src/Shapes/Shape.cpp
src/Shapes/Shape.hpp
src/Shapes/ShapeOps_impl.hpp
src/Shapes/Shape_impl.hpp
src/unittests/ShapeUnittest.cpp

• AtomShapeDescriptor had been implemented doubly.
• LineSegment* moved to LinearAlgebra/
• BaseShapes:: Cuboid is from (0,0,0) and not from (-1,-1,-1) to (1,1,1)
  • had to fix ShapeUnittest
• some overlap in Shapes due to getHomogeneousPointsOnSurface added in stable.
• BUGFIX: Matrix::transpose() did not allocate MatrixContent::content.
• merged BaseShapesUnitTest into ShapeUnitTest.

File:

• src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (4 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 "log.hpp"
+#include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
 #include "molecule.hpp"
-#include "Descriptors/MoleculeDescriptor.hpp"
 #include "stackclass.hpp"
 #include "World.hpp"
@@ -21 +36 @@
 #include <string>
 
+typedef std::map< moleculeId_t, std::vector<atomId_t> > MolAtomList;
+typedef std::map< atomId_t, atomId_t > AtomAtomList;
+
 using namespace std;
 
-#include "UIElements/UIFactory.hpp"
-#include "UIElements/Dialog.hpp"
-#include "UIElements/ValueStorage.hpp"
-
-const char FragmentationSubgraphDissectionAction::NAME[] = "subgraph-dissect";
-
-FragmentationSubgraphDissectionAction::FragmentationSubgraphDissectionAction() :
-  Action(NAME)
-{}
-
-FragmentationSubgraphDissectionAction::~FragmentationSubgraphDissectionAction()
-{}
-
-void FragmentationSubgraphDissection() {
-  ActionRegistry::getInstance().getActionByName(FragmentationSubgraphDissectionAction::NAME)->call(Action::NonInteractive);
-};
-
-Dialog* FragmentationSubgraphDissectionAction::createDialog() {
-  Dialog *dialog = UIFactory::getInstance().makeDialog();
-
-  dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
-
-  return dialog;
-}
-
-
+#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
+
+// and construct the stuff
+#include "SubgraphDissectionAction.def"
+#include "Action_impl_pre.hpp"
+/** =========== define the function ====================== */
 Action::state_ptr FragmentationSubgraphDissectionAction::performCall() {
+  // obtain information
+  getParametersfromValueStorage();
+
   DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
-  // @TODO rather do the dissection afterwards
+
+  // first create stuff for 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, params);
+
+  // 0a. remove all present molecules
   MoleculeListClass *molecules = World::getInstance().getMolecules();
-  molecules->DissectMoleculeIntoConnectedSubgraphs(World::getInstance().getPeriode(), World::getInstance().getConfig());
-  return Action::success;
+  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();
+  int BondCount = 0;
+  {
+    vector <atom *> allatoms = World::getInstance().getAllAtoms();
+    for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
+      BondCount += (*AtomRunner)->ListOfBonds.size();
+//      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 (BondCount == 0) {
+    config * const configuration = World::getInstance().getConfig();
+    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
+  {
+    {
+      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->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->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
+  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);
+
+  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
+    MoleculeListClass *molecules = World::getInstance().getMolecules();
+    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) {
+        atom *Walker = World::getInstance().getAtom(AtomById(*atomiter));
+        mol->AddAtom(Walker);
+      }
+      molecules->insert(mol);
+    }
+  }
+
+  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;
 }
 
@@ -82 +216 @@
   return NAME;
 }
+/** =========== end of function ====================== */