Changeset 87f6c9 for src

Timestamp:

May 8, 2008, 3:39:36 PM (17 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:

bf46da

Parents:

da5355

Message:

new function MoleculeLeafClass::TranslateIndicesToGlobalIDs() used in molecule::FragmentMolecule()

MoleculeLeafClass::TranslateIndicesToGlobalIDs() abstractizes translation of local atom::nr returned by BOSSANOVA per fragment into one list of global indices that can be used to store fragment configs and globally valid keyset file

Location:

src

Files:

• moleculelist.cpp (modified) (1 diff)
• molecules.cpp (modified) (1 diff)
• molecules.hpp (modified) (1 diff)

src/moleculelist.cpp

@@ -540 +540 @@
 };
 
+/** Translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
+ * \param *out output stream for debugging
+ * \param **FragmentList Graph with local numbers per fragment
+ * \param &FragmentCounter counts the fragments as we move along the list
+ * \param &TotalNumberOfKeySets global key set counter
+ * \param &TotalGraph Graph to be filled with global numbers
+ */ 
+void MoleculeLeafClass::TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
+{
+  KeySet *TempSet = new KeySet;
+  for(Graph::iterator runner = FragmentList[FragmentCounter]->begin(); runner != FragmentList[FragmentCounter]->end(); runner++) {
+    for(KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
+      TempSet->insert((Leaf->FindAtom(*sprinter))->GetTrueFather()->nr);
+    TotalGraph.insert(GraphPair(*TempSet, pair<int,double>(TotalNumberOfKeySets++, (*runner).second.second)));
+    TempSet->clear();
+  }
+  delete(TempSet);
+  if (next != NULL)
+    next->TranslateIndicesToGlobalIDs(out, FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
+  FragmentCounter--;
+};
+
 /** Simply counts the number of items in the list, from given MoleculeLeafClass.
  * \return number of items

src/molecules.cpp

@@ -2273 +2273 @@
 
   // ===== 8a. translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
-  MolecularWalker = Subgraphs;
-  FragmentCounter = 0;
-  while (MolecularWalker->next != NULL) {
-    MolecularWalker = MolecularWalker->next;
-    KeySet *TempSet = new KeySet;
-    for(Graph::iterator runner = FragmentList[FragmentCounter]->begin(); runner != FragmentList[FragmentCounter]->end(); runner++) {
-      for(KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
-        TempSet->insert((MolecularWalker->Leaf->FindAtom(*sprinter))->GetTrueFather()->nr);
-      TotalGraph.insert(GraphPair(*TempSet, pair<int,double>(TotalNumberOfKeySets++, (*runner).second.second)));
-      TempSet->clear();
-    }
-    delete(TempSet);
-    delete(FragmentList[FragmentCounter]);
-    FragmentCounter++;
-  }
-  Free((void **)&FragmentList, "molecule::FragmentMolecule - **FragmentList");
+  Subgraphs->next->TranslateIndicesToGlobalIDs(out, FragmentList, (FragmentCounter = 0), TotalNumberOfKeySets, TotalGraph);
+  
   // free subgraph memory again
   delete(ParsedFragmentList);
+  FragmentCounter = 0;
   if (Subgraphs != NULL) {
     while (Subgraphs->next != NULL) {
       Subgraphs = Subgraphs->next;
+      delete(FragmentList[FragmentCounter++]);
       delete(Subgraphs->previous);
     }
     delete(Subgraphs);
   }
+  Free((void **)&FragmentList, "molecule::FragmentMolecule - **FragmentList");
 
   // ===== 8b. gather keyset lists (graphs) from all subgraphs and transform into MoleculeListClass =====

src/molecules.hpp

@@ -414 +414 @@
   bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
   bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, int &FragmentCounter, int GlobalAtomCount, bool &FreeList);
+  void TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
   int Count() const;
 };