Changeset 8540f0

Timestamp:

Jun 8, 2010, 1:57:09 PM (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:

c78d44

Parents:

e4b5de

Message:

Case 'D' is now handled by CommandLineUI.

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (1 diff)
• builder.cpp (modified) (1 diff)

src/Actions/MapOfActions.cpp

@@ -239 +239 @@
 //  generic.insert("convex-envelope");
 //      generic.insert("default-molname");
-//      generic.insert("depth-first-search");
+        generic.insert("depth-first-search");
 //      generic.insert("element-db");
 //      generic.insert("fastparsing");

src/builder.cpp

@@ -1729 +1729 @@
             case 'D':
               if (ExitFlag == 0) ExitFlag = 1;
-              {
-                DoLog(1) && (Log() << Verbose(1) << "Depth-First-Search Analysis." << endl);
-                MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
-                int *MinimumRingSize = new int[mol->getAtomCount()];
-                atom ***ListOfLocalAtoms = NULL;
-                class StackClass<bond *> *BackEdgeStack = NULL;
-                class StackClass<bond *> *LocalBackEdgeStack = NULL;
-                mol->CreateAdjacencyList(atof(argv[argptr]), configuration.GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
-                Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
-                if (Subgraphs != NULL) {
-                  int FragmentCounter = 0;
-                  while (Subgraphs->next != NULL) {
-                    Subgraphs = Subgraphs->next;
-                    Subgraphs->FillBondStructureFromReference(mol, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
-                    LocalBackEdgeStack = new StackClass<bond *> (Subgraphs->Leaf->BondCount);
-                    Subgraphs->Leaf->PickLocalBackEdges(ListOfLocalAtoms[FragmentCounter], BackEdgeStack, LocalBackEdgeStack);
-                    Subgraphs->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);
-                    delete(LocalBackEdgeStack);
-                    delete(Subgraphs->previous);
-                    FragmentCounter++;
-                  }
-                  delete(Subgraphs);
-                  for (int i=0;i<FragmentCounter;i++)
-                    delete[](ListOfLocalAtoms[i]);
-                  delete[](ListOfLocalAtoms);
-                }
-                delete(BackEdgeStack);
-                delete[](MinimumRingSize);
-              }
-              //argptr+=1;
+              ArgcList.insert(argptr-1);
+              ArgcList.insert(argptr);
+              argptr+=1;
               break;
             case 'I':