Changeset 2b7d1b for src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

Timestamp:

Aug 11, 2010, 4:31:34 PM (14 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:

701ad6, fa7989

Parents:

31fb1d

git-author:

Frederik Heber <heber@…> (07/29/10 12:07:40)

git-committer:

Frederik Heber <heber@…> (08/11/10 16:31:34)

Message:

Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.

• also rewrote the function a bit:
  • no more copying of atoms
  • we just take the molecule out of the MoleculeLeafs
  • molecule that contains all atoms is destroyed including all original atoms (they are copied by DFS).

File:

• src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (6 diffs)

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -24 +24 @@
 #include "molecule.hpp"
 #include "stackclass.hpp"
+#include "verbose.hpp"
 #include "World.hpp"
 
@@ -44 +45 @@
 {}
 
+/** 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);
@@ -59 +62 @@
 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
+
   MoleculeListClass *molecules = World::getInstance().getMolecules();
   config * const configuration = World::getInstance().getConfig();
@@ -101 +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
@@ -143 +147 @@
   // 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();
+
+  // 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 = MolecularWalker->next;
@@ -156 +171 @@
   }
   delete(MolecularWalker);
+<<<<<<< HEAD
   delete[](moleculelist);
+=======
+>>>>>>> Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.
   DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);