Changeset a564be for src/Actions

Timestamp:

Dec 6, 2010, 7:37:05 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:

4c1230

Parents:

fd19ff

git-author:

Frederik Heber <heber@…> (12/06/10 19:15:03)

git-committer:

Frederik Heber <heber@…> (12/06/10 19:37:05)

Message:

Removed ancient StackClass, replaced by std::deque.

• all PopLast replaced by pop_front.
• all PopFirst replaced by pop_front.
• and we have two remove items in two steps, first get item, then pop.

Location:

src/Actions/FragmentationAction

Files:

• DepthFirstSearchAction.cpp (modified) (3 diffs)
• FragmentationAction.cpp (modified) (1 diff)
• SubgraphDissectionAction.cpp (modified) (2 diffs)

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -24 +24 @@
 #include "config.hpp"
 #include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
 #include "molecule.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
-#include "stackclass.hpp"
-#include "Helpers/Verbose.hpp"
 #include "World.hpp"
 
@@ -51 +50 @@
   int *MinimumRingSize = new int[mol->getAtomCount()];
   atom **ListOfAtoms = NULL;
-  class StackClass<bond *> *BackEdgeStack = NULL;
-  class StackClass<bond *> *LocalBackEdgeStack = NULL;
+  std::deque<bond *> *BackEdgeStack = NULL;
+  std::deque<bond *> *LocalBackEdgeStack = NULL;
   mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
@@ -61 +60 @@
       ListOfAtoms = NULL;
       Subgraphs->FillBondStructureFromReference(mol, ListOfAtoms, false);  // we want to keep the created ListOfLocalAtoms
-      LocalBackEdgeStack = new StackClass<bond *> (Subgraphs->Leaf->BondCount);
+      LocalBackEdgeStack = new std::deque<bond *>; // no need to have it Subgraphs->Leaf->BondCount size
       Subgraphs->Leaf->PickLocalBackEdges(ListOfAtoms, BackEdgeStack, LocalBackEdgeStack);
       Subgraphs->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -24 +24 @@
 #include "config.hpp"
 #include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
 #include "molecule.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
-#include "stackclass.hpp"
 #include "World.hpp"
 

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -30 +30 @@
 #include "Helpers/Verbose.hpp"
 #include "molecule.hpp"
-#include "stackclass.hpp"
 #include "World.hpp"
 
@@ -103 +102 @@
   // 2. scan for connected subgraphs
   MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
-  class StackClass<bond *> *BackEdgeStack = NULL;
+  std::deque<bond *> *BackEdgeStack = NULL;
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
   delete(BackEdgeStack);