Changeset 6d551c for src/Graph

Timestamp:

Oct 26, 2012, 1:24:01 PM (12 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:

f96874

Parents:

dbe3b9

git-author:

Frederik Heber <heber@…> (09/07/12 08:47:35)

git-committer:

Frederik Heber <heber@…> (10/26/12 13:24:01)

Message:

ListOfLocalAtoms is now a map, inherited into a distinct class.

• this is preparatory for allowing arbitrary fragmentation of atoms not only of a single molecule.

Location:

src/Graph

Files:

• DepthFirstSearchAnalysis.cpp (modified) (4 diffs)
• DepthFirstSearchAnalysis.hpp (modified) (2 diffs)
• ListOfLocalAtoms.hpp (added)
• Makefile.am (modified) (1 diff)

src/Graph/DepthFirstSearchAnalysis.cpp

@@ -48 +48 @@
 #include "Descriptors/AtomDescriptor.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
+#include "Graph/ListOfLocalAtoms.hpp"
 #include "molecule.hpp"
 #include "MoleculeLeafClass.hpp"
@@ -121 +122 @@
 
 
-bool DepthFirstSearchAnalysis::PickLocalBackEdges(atom **ListOfLocalAtoms, std::deque<bond *> *&LocalStack) const
+bool DepthFirstSearchAnalysis::PickLocalBackEdges(const ListOfLocalAtoms_t &ListOfLocalAtoms, std::deque<bond *> *&LocalStack) const
 {
   bool status = true;
@@ -133 +134 @@
 
   do { // go through all bonds and push local ones
-    Walker = ListOfLocalAtoms[Binder->leftatom->getNr()]; // get one atom in the reference molecule
+    const ListOfLocalAtoms_t::const_iterator leftiter = ListOfLocalAtoms.find(Binder->leftatom->getNr());
+    ASSERT( leftiter != ListOfLocalAtoms.end(),
+        "DepthFirstSearchAnalysis::PickLocalBackEdges() - could not find atom id "
+        +toString(Binder->leftatom->getNr())+" in ListOfLocalAtoms.");
+    Walker = leftiter->second; // get one atom in the reference molecule
     if (Walker != NULL) { // if this Walker exists in the subgraph ...
       const BondList& ListOfBonds = Walker->getListOfBonds();
@@ -140 +145 @@
           ++Runner) {
         OtherAtom = (*Runner)->GetOtherAtom(Walker);
-        if (OtherAtom == ListOfLocalAtoms[(*Runner)->rightatom->getNr()]) { // found the bond
+        const ListOfLocalAtoms_t::const_iterator rightiter = ListOfLocalAtoms.find((*Runner)->rightatom->getNr());
+        if (OtherAtom == rightiter->second) { // found the bond
           LocalStack->push_front((*Runner));
           LOG(3, "INFO: Found local edge " << *(*Runner) << ".");

src/Graph/DepthFirstSearchAnalysis.hpp

@@ -20 +20 @@
 class atom;
 class bond;
+class ListOfLocalAtoms_t;
 class MoleculeLeafClass;
 class molecule;
@@ -66 +67 @@
    * Reference is the internal BackEdgeStack.
    *
-   * \param **ListOfLocalAtoms array of father atom::nr to local atom::nr (reverse of atom::father)
+   * \param ListOfLocalAtoms array of father atom::nr to local atom::nr (reverse of atom::father)
    * \param *LocalStack stack to be filled
    * \return true - everything ok, false - ReferenceStack was empty
    */
-  bool PickLocalBackEdges(atom **ListOfLocalAtoms, std::deque<bond *> *&LocalStack) const;
+  bool PickLocalBackEdges(const ListOfLocalAtoms_t &ListOfLocalAtoms, std::deque<bond *> *&LocalStack) const;
 
   /** Getter for BackEdgeStack.

src/Graph/Makefile.am

@@ -18 +18 @@
         Graph/ConnectedSubgraph.hpp \
         Graph/CyclicStructureAnalysis.hpp \
-        Graph/DepthFirstSearchAnalysis.hpp
+        Graph/DepthFirstSearchAnalysis.hpp \
+        Graph/ListOfLocalAtoms.hpp