Changeset ec87e4 for src/molecule_fragmentation.cpp

Timestamp:

Oct 25, 2011, 12:08:02 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

708798

Parents:

5fd0f4

git-author:

Frederik Heber <heber@…> (10/17/11 15:23:42)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:02)

Message:

Rewrite of CheckAgainstAdjacencyFile.

• we now construct two multimaps -- one from file, the other from World's selected atoms -- and compare these two.
• added unit test on the class.

File:

• src/molecule_fragmentation.cpp (modified) (1 diff)

src/molecule_fragmentation.cpp

@@ -659 +659 @@
   {
     std::ifstream File;
-    string filename;
+    std::string filename;
     filename = prefix + ADJACENCYFILE;
     File.open(filename.c_str(), ios::out);
     DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl);
-    std::map<int, atom*> ListOfAtoms;
-    std::pair<std::map<int, atom*>::iterator, bool> inserter;
-    for (const_iterator iter = begin();
-        iter != end();
-        ++iter) {
-      atom *Walker = *iter;
-      inserter = ListOfAtoms.insert( make_pair( Walker->GetTrueFather()->getNr(), Walker) );
-      FragmentationToDo = FragmentationToDo && inserter.second;
-    }
-    CheckAgainstAdjacencyFile FileChecker;
-    FragmentationToDo = FragmentationToDo && FileChecker(File, ListOfAtoms);
+
+    CheckAgainstAdjacencyFile FileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
+    FragmentationToDo = FragmentationToDo && FileChecker(File);
   }