Changeset 2d4334

Timestamp:

Mar 7, 2011, 11:40:27 AM (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:

13a953

Parents:

dda246

git-author:

Frederik Heber <heber@…> (03/03/11 00:11:14)

git-committer:

Frederik Heber <heber@…> (03/07/11 11:40:27)

Message:

Moved BuildInducedSubgraph from molecule into functor in Graph/.

• BuildInducedSubgraph::ParentList has been reworked into map<atom*,atom*>.

Location:

src

Files:

• Graph/BuildInducedSubgraph.cpp (added)
• Graph/BuildInducedSubgraph.hpp (added)
• Graph/Makefile.am (modified) (2 diffs)
• molecule.hpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)

src/Graph/Makefile.am ¶

@@ -9 +9 @@
 GRAPHSOURCE = \
         BreadthFirstSearchAdd.cpp \
+        BuildInducedSubgraph.cpp \
         ConnectedSubgraph.cpp \
         CyclicStructureAnalysis.cpp \
@@ -15 +16 @@
 GRAPHHEADER = \
         BreadthFirstSearchAdd.hpp \
+        BuildInducedSubgraph.hpp \
         ConnectedSubgraph.hpp \
         CyclicStructureAnalysis.hpp \

src/molecule.hpp ¶

@@ -226 +226 @@
   void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack);
   int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
-  bool BuildInducedSubgraph(const molecule *Father);
   molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
   void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, std::vector<bond *> &BondsSet, int SetDimension, int SubOrder);

src/molecule_graph.cpp ¶

@@ -327 +327 @@
 ;
 
-void BuildInducedSubgraph_Init(atom **&ParentList, int AtomCount)
-{
-  // reset parent list
-  ParentList = new atom*[AtomCount];
-  for (int i=0;i<AtomCount;i++)
-    ParentList[i] = NULL;
-  DoLog(3) && (Log() << Verbose(3) << "Resetting ParentList." << endl);
-}
-;
-
-void BuildInducedSubgraph_FillParentList(const molecule *mol, const molecule *Father, atom **&ParentList)
-{
-  // fill parent list with sons
-  DoLog(3) && (Log() << Verbose(3) << "Filling Parent List." << endl);
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    ParentList[(*iter)->father->getNr()] = (*iter);
-    // Outputting List for debugging
-    DoLog(4) && (Log() << Verbose(4) << "Son[" << (*iter)->father->getNr() << "] of " << (*iter)->father << " is " << ParentList[(*iter)->father->getNr()] << "." << endl);
-  }
-};
-
-void BuildInducedSubgraph_Finalize(atom **&ParentList)
-{
-  delete[](ParentList);
-}
-;
-
-bool BuildInducedSubgraph_CreateBondsFromParent(molecule *mol, const molecule *Father, atom **&ParentList)
-{
-  bool status = true;
-  atom *OtherAtom = NULL;
-  // check each entry of parent list and if ok (one-to-and-onto matching) create bonds
-  DoLog(3) && (Log() << Verbose(3) << "Creating bonds." << endl);
-  for (molecule::const_iterator iter = Father->begin(); iter != Father->end(); ++iter) {
-    if (ParentList[(*iter)->getNr()] != NULL) {
-      if (ParentList[(*iter)->getNr()]->father != (*iter)) {
-        status = false;
-      } else {
-        const BondList& ListOfBonds = (*iter)->getListOfBonds();
-        for (BondList::const_iterator Runner = ListOfBonds.begin();
-            Runner != ListOfBonds.end();
-            ++Runner) {
-          OtherAtom = (*Runner)->GetOtherAtom((*iter));
-          if (ParentList[OtherAtom->getNr()] != NULL) { // if otheratom is also a father of an atom on this molecule, create the bond
-            DoLog(4) && (Log() << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[(*iter)->getNr()]->getName() << " and " << ParentList[OtherAtom->getNr()]->getName() << "." << endl);
-            mol->AddBond(ParentList[(*iter)->getNr()], ParentList[OtherAtom->getNr()], (*Runner)->BondDegree);
-          }
-        }
-      }
-    }
-  }
-  return status;
-}
-;
-
-/** Adds bond structure to this molecule from \a Father molecule.
- * This basically causes this molecule to become an induced subgraph of the \a Father, i.e. for every bond in Father
- * with end points present in this molecule, bond is created in this molecule.
- * Special care was taken to ensure that this is of complexity O(N), where N is the \a Father's molecule::AtomCount.
- * \param *Father father molecule
- * \return true - is induced subgraph, false - there are atoms with fathers not in \a Father
- * \todo not checked, not fully working probably
- */
-bool molecule::BuildInducedSubgraph(const molecule *Father){
-  bool status = true;
-  atom **ParentList = NULL;
-  DoLog(2) && (Log() << Verbose(2) << "Begin of BuildInducedSubgraph." << endl);
-  BuildInducedSubgraph_Init(ParentList, Father->getAtomCount());
-  BuildInducedSubgraph_FillParentList(this, Father, ParentList);
-  status = BuildInducedSubgraph_CreateBondsFromParent(this, Father, ParentList);
-  BuildInducedSubgraph_Finalize(ParentList);
-  DoLog(2) && (Log() << Verbose(2) << "End of BuildInducedSubgraph." << endl);
-  return status;
-}
-;
-
 /** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
  * \param **&ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled