Changeset 701ad6

Timestamp:

Aug 28, 2010, 1:36:03 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:

653542

Parents:

2b7d1b

git-author:

Frederik Heber <heber@…> (08/28/10 01:31:44)

git-committer:

Frederik Heber <heber@…> (08/28/10 01:36:03)

Message:

FIX: Merge stuff still left inside.

File:

• src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (2 diffs)

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp ¶

@@ -22 +22 @@
 #include "config.hpp"
 #include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
 #include "molecule.hpp"
 #include "stackclass.hpp"
-#include "verbose.hpp"
 #include "World.hpp"
 
@@ -104 +104 @@
     return Action::failure;
   }
-<<<<<<< HEAD
-
-  // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
-  // the original one as parsed in)
-  // TODO: Optimize this, when molecules just contain pointer list of global atoms!
-
-  // 4a. create array of molecules to fill
-  const int MolCount = Subgraphs->next->Count();
-  char number[MAXSTRINGSIZE];
-  molecule **moleculelist = new molecule *[MolCount];
-  MoleculeLeafClass *MolecularWalker = Subgraphs;
-  for (int i=0;i<MolCount;i++) {
-    MolecularWalker = MolecularWalker->next;
-    moleculelist[i] = World::getInstance().createMolecule();
-    moleculelist[i]->ActiveFlag = true;
-    strncpy(moleculelist[i]->name, mol->name, MAXSTRINGSIZE);
-    if (MolCount > 1) {
-      sprintf(number, "-%d", i+1);
-      strncat(moleculelist[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
-    }
-    DoLog(1) && (Log() << Verbose(1) << "MolName is " << moleculelist[i]->name << ", id is " << moleculelist[i]->getId() << endl);
-    for (molecule::iterator iter = MolecularWalker->Leaf->begin(); iter != MolecularWalker->Leaf->end(); ++iter) {
-      DoLog(1) && (Log() << Verbose(1) << **iter << endl);
-    }
-    molecules->insert(moleculelist[i]);
-  }
-
-  // 4b. create and fill map of which atom is associated to which connected molecule (note, counting starts at 1)
-  int FragmentCounter = 0;
-  map<int, atom *> AtomToFragmentMap;
-  MolecularWalker = Subgraphs;
-  while (MolecularWalker->next != NULL) {
-    MolecularWalker = MolecularWalker->next;
-    for (molecule::iterator iter = MolecularWalker->Leaf->begin(); !MolecularWalker->Leaf->empty(); iter = MolecularWalker->Leaf->begin()) {
-      atom * Walker = *iter;
-      DoLog(1) && (Log() << Verbose(1) << "Re-linking " << Walker << "..." << endl);
-      MolecularWalker->Leaf->erase(iter);
-      moleculelist[FragmentCounter]->AddAtom(Walker);    // counting starts at 1
-    }
-    FragmentCounter++;
-  }
-  // TODO: When DepthFirstSearchAnalysis does not use AddCopyAtom() anymore, we don't need to delete all original atoms.
-  // 4d. destroy the original molecule
-=======
-  int FragmentCounter = Subgraphs->Count();
+  int FragmentCounter = Subgraphs->next->Count();
 
   // TODO: When DepthFirstSearchAnalysis does not use AddCopyAtom() anymore, we don't need to delete all original atoms
   // 3. destroy the original molecule
->>>>>>> Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.
   for (molecule::iterator AtomRunner = mol->begin(); !mol->empty(); AtomRunner = mol->begin())
     World::getInstance().destroyAtom(*AtomRunner);
   World::getInstance().destroyMolecule(mol);
 
-<<<<<<< HEAD
-  // 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
-  // TODO: check whether this is really not needed anymore
-  // 4e. free Leafs
-  MolecularWalker = Subgraphs;
-=======
   // 4. free Leafs
   MoleculeLeafClass *MolecularWalker = Subgraphs;
->>>>>>> Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.
   while (MolecularWalker->next != NULL) {
+    MolecularWalker->Leaf = NULL;
     MolecularWalker = MolecularWalker->next;
     delete(MolecularWalker->previous);
   }
   delete(MolecularWalker);
-<<<<<<< HEAD
-  delete[](moleculelist);
-=======
->>>>>>> Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.
   DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);