Changeset fd4905 for src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

Timestamp:

Aug 28, 2010, 1:45:13 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:

6c438f

Parents:

8fd934 (diff), 653542 (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.

Message:

Merge branch 'stable' into StructureRefactoring

File:

• src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (10 diffs)

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -20 +20 @@
 #include "Helpers/MemDebug.hpp"
 
-#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
-#include "Actions/ActionRegistry.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
@@ -38 +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 "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";
-
-FragmentationSubgraphDissectionAction::FragmentationSubgraphDissectionAction() :
-  Action(NAME)
-{}
-
-FragmentationSubgraphDissectionAction::~FragmentationSubgraphDissectionAction()
-{}
-
-/** 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);
-};
-
-Dialog* FragmentationSubgraphDissectionAction::fillDialog(Dialog *dialog) {
-  ASSERT(dialog,"No Dialog given when filling action dialog");
-
-  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);
 
-  // first create undo state
+  // first create stuff for undo state
   MolAtomList moleculelist;
   vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
@@ -94 +64 @@
     moleculelist.insert( std::pair< moleculeId_t, std::vector<atomId_t> > ((*moliter)->getId(), atomlist));
   }
-  FragmentationSubgraphDissectionState *UndoState = new FragmentationSubgraphDissectionState(moleculelist);
-
+  FragmentationSubgraphDissectionState *UndoState = new FragmentationSubgraphDissectionState(moleculelist, params);
+
+  // 0a. remove all present molecules
   MoleculeListClass *molecules = World::getInstance().getMolecules();
-  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);
@@ -107 +75 @@
   // 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) {
-      for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
-        delete(*BondRunner);
+      BondCount += (*AtomRunner)->ListOfBonds.size();
+//      for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+//        delete(*BondRunner);
       mol->AddAtom(*AtomRunner);
     }
@@ -117 +87 @@
 
   // 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);
+  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;
     }
-  } else {
-    DoeLog(1) && (eLog()<< Verbose(1) << "There is no BondGraph class present to create bonds." << endl);
-    return Action::failure;
   }
 
@@ -138 +111 @@
     return Action::failure;
   }
-  int FragmentCounter = Subgraphs->next->Count();
+
+  //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).
+    {
+      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();
-    for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
-      (*AtomRunner)->father = *AtomRunner;
+    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;
+      }
     }
   }
@@ -162 +164 @@
   MolecularWalker->Leaf = NULL;
   delete(MolecularWalker);
-  DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);
+  DoLog(1) && (Log() << Verbose(1) << "I scanned " << molecules->ListOfMolecules.size() << " molecules." << endl);
 
   return Action::state_ptr(UndoState);
@@ -182 +184 @@
   {
     // 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) {
@@ -187 +190 @@
       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)));
+      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);
     }
   }
@@ -210 +216 @@
   return NAME;
 }
+/** =========== end of function ====================== */