Changeset 0b05147

Timestamp:

May 9, 2008, 2:38:27 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:

98b1d2

Parents:

fc850d

Message:

CyclicStructureAnalysis(): forget to check whether we actually have found rings or not (only then MinimumRingSize needs to be checked for non-set neighbours also)

File:

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

src/molecules.cpp

@@ -1735 +1735 @@
     }
   }
-  // go over all atoms 
-  Root = start;
-  while(Root->next != end) {
-    Root = Root->next;
+  if (MinRingSize != -1) {
+    // go over all atoms 
+    Root = start;
+    while(Root->next != end) {
+      Root = Root->next;
+      
+      if (MinimumRingSize[Root->GetTrueFather()->nr] == AtomCount) { // check whether MinimumRingSize is set, if not BFS to next where it is
+        ShortestPathList[Walker->nr] = 0;
+        BFSStack->ClearStack();  // start with empty BFS stack
+        BFSStack->Push(Walker);
+        TouchedStack->Push(Walker);
+        //*out << Verbose(1) << "---------------------------------------------------------------------------------------------------------" << endl;
+        OtherAtom = Walker;
+        while ((Walker != Root) && (OtherAtom != NULL)) {  // look for Root
+          Walker = BFSStack->PopFirst();
+          //*out << Verbose(2) << "Current Walker is " << *Walker << ", we look for SP to Root " << *Root << "." << endl;
+          for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {
+            Binder = ListOfBondsPerAtom[Walker->nr][i];
+            if (Binder != BackEdge) { // only walk along DFS spanning tree (otherwise we always find SP of one being backedge Binder)
+              OtherAtom = Binder->GetOtherAtom(Walker);
+              //*out << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *Binder << "." << endl;
+              if (ColorList[OtherAtom->nr] == white) {
+                TouchedStack->Push(OtherAtom);
+                ColorList[OtherAtom->nr] = lightgray;
+                PredecessorList[OtherAtom->nr] = Walker;  // Walker is the predecessor
+                ShortestPathList[OtherAtom->nr] = ShortestPathList[Walker->nr]+1;
+                //*out << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " lightgray, its predecessor is " << Walker->Name << " and its Shortest Path is " << ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl;
+                if (MinimumRingSize[OtherAtom->GetTrueFather()->nr] != AtomCount) { // if the other atom is connected to a ring
+                  MinimumRingSize[Root->GetTrueFather()->nr] = ShortestPathList[OtherAtom->nr]+MinimumRingSize[OtherAtom->GetTrueFather()->nr];
+                  OtherAtom = NULL; //break;
+                  break;
+                } else
+                  BFSStack->Push(OtherAtom);
+              } else {
+                //*out << Verbose(3) << "Not Adding, has already been visited." << endl;
+              }
+            } else {
+              //*out << Verbose(3) << "Not Visiting, is a back edge." << endl;
+            }
+          }
+          ColorList[Walker->nr] = black;
+          //*out << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl; 
+        }
     
-    if (MinimumRingSize[Root->GetTrueFather()->nr] == AtomCount) { // check whether MinimumRingSize is set, if not BFS to next where it is
-      ShortestPathList[Walker->nr] = 0;
-      BFSStack->ClearStack();  // start with empty BFS stack
-      BFSStack->Push(Walker);
-      TouchedStack->Push(Walker);
-      //*out << Verbose(1) << "---------------------------------------------------------------------------------------------------------" << endl;
-      OtherAtom = Walker;
-      while ((Walker != Root) && (OtherAtom != NULL)) {  // look for Root
-        Walker = BFSStack->PopFirst();
-        //*out << Verbose(2) << "Current Walker is " << *Walker << ", we look for SP to Root " << *Root << "." << endl;
-        for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {
-          Binder = ListOfBondsPerAtom[Walker->nr][i];
-          if (Binder != BackEdge) { // only walk along DFS spanning tree (otherwise we always find SP of one being backedge Binder)
-            OtherAtom = Binder->GetOtherAtom(Walker);
-            //*out << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *Binder << "." << endl;
-            if (ColorList[OtherAtom->nr] == white) {
-              TouchedStack->Push(OtherAtom);
-              ColorList[OtherAtom->nr] = lightgray;
-              PredecessorList[OtherAtom->nr] = Walker;  // Walker is the predecessor
-              ShortestPathList[OtherAtom->nr] = ShortestPathList[Walker->nr]+1;
-              //*out << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " lightgray, its predecessor is " << Walker->Name << " and its Shortest Path is " << ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl;
-              if (MinimumRingSize[OtherAtom->GetTrueFather()->nr] != AtomCount) { // if the other atom is connected to a ring
-                MinimumRingSize[Root->GetTrueFather()->nr] = ShortestPathList[OtherAtom->nr]+MinimumRingSize[OtherAtom->GetTrueFather()->nr];
-                OtherAtom = NULL; //break;
-                break;
-              } else
-                BFSStack->Push(OtherAtom);
-            } else {
-              //*out << Verbose(3) << "Not Adding, has already been visited." << endl;
-            }
-          } else {
-            //*out << Verbose(3) << "Not Visiting, is a back edge." << endl;
-          }
+        // now clean the lists
+        while (!TouchedStack->IsEmpty()){
+          Walker = TouchedStack->PopFirst();
+          PredecessorList[Walker->nr] = NULL;
+          ShortestPathList[Walker->nr] = -1;
+          ColorList[Walker->nr] = white;
         }
-        ColorList[Walker->nr] = black;
-        //*out << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl; 
-      }
-
-      // now clean the lists
-      while (!TouchedStack->IsEmpty()){
-        Walker = TouchedStack->PopFirst();
-        PredecessorList[Walker->nr] = NULL;
-        ShortestPathList[Walker->nr] = -1;
-        ColorList[Walker->nr] = white;
-      }
-    }
-    *out << Verbose(1) << "Minimum ring size of " << *Root << " is " << MinimumRingSize[Root->GetTrueFather()->nr] << "." << endl;
-  }
-  
-        
-  if (MinRingSize != -1)
+      }
+      *out << Verbose(1) << "Minimum ring size of " << *Root << " is " << MinimumRingSize[Root->GetTrueFather()->nr] << "." << endl;
+    }
     *out << Verbose(1) << "Minimum ring size is " << MinRingSize << ", over " << NumCycles << " cycles total." << endl;
-  else
+  } else
     *out << Verbose(1) << "No rings were detected in the molecular structure." << endl;