Changeset ae38fb for src/config.cpp

Timestamp:

Nov 3, 2009, 2:34:02 PM (16 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, 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:

3c349b

Parents:

2aeefd

git-author:

Frederik Heber <heber@…> (11/03/09 14:27:15)

git-committer:

Frederik Heber <heber@…> (11/03/09 14:34:02)

Message:

Fixing not created adjacency list, partially fixing subgraph dissection in config::Load()

• CreateAdjacencyList() was called with zero bonddistance.
• this was due to max_distance not being initialised in the constructor to 0 and subsequently not set if Bond Length Table was not found.
• new function SetMaxDistanceToMaxOfCovalentRadii() which sets the max_distance to twice the max of covalent radii of all elements.
• config::Load() - atoms in copied molecule (by DepthFirstSearchAnalysis()) are made their own father (and originals are removed).

File:

• src/config.cpp (modified) (1 diff)

src/config.cpp

@@ -1051 +1051 @@
   } else {
     cout << Verbose(0) << "Bond length table loading failed." << endl;
+    BG->SetMaxDistanceToMaxOfCovalentRadii((ofstream *)&cout, periode);
   }
 
   // 3. parse the molecule in
   LoadMolecule(mol, FileBuffer, periode, FastParsing);
-  mol->ActiveFlag = true;
-  MolList->insert(mol);
+  //mol->ActiveFlag = true;
+  //MolList->insert(mol);
 
   // 4. dissect the molecule into connected subgraphs
   BG->ConstructBondGraph((ofstream *)&cout, mol);
+
+  // 5. scan for connected subgraphs
+  MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
+  class StackClass<bond *> *BackEdgeStack = NULL;
+  Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, BackEdgeStack);
+  delete(BackEdgeStack);
+
+  // 6. dissect
+  atom ***ListOfLocalAtoms = NULL;
+  int FragmentCounter = 0;
+  MoleculeLeafClass *MolecularWalker = Subgraphs;
+  atom *Walker = NULL;
+  while (MolecularWalker->next != NULL) {
+    MolecularWalker = MolecularWalker->next;
+    // fill the bond structure of the individually stored subgraphs (goes through whole chained list by itself)
+    MolecularWalker->FillBondStructureFromReference((ofstream *)&cout, mol, FragmentCounter, ListOfLocalAtoms, false);  // we don't want to keep the created ListOfLocalAtoms
+    FragmentCounter++;
+    MolecularWalker->Leaf->ActiveFlag = true;
+    Walker = MolecularWalker->Leaf->start;
+    while (Walker->next != MolecularWalker->Leaf->end) {
+      Walker = Walker->next;
+      Walker->father = Walker;
+    }
+    MolList->insert(MolecularWalker->Leaf);
+    MolecularWalker->Leaf = NULL; // don't remove molecule when deleting MolecularWalker
+    delete(MolecularWalker->previous);
+  }
+  delete(MolecularWalker);
+  for (int i=0;i<FragmentCounter;i++)
+    Free(&ListOfLocalAtoms[i]);
+  Free(&ListOfLocalAtoms);
+  cout << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl;
+
+  // 6. free parsed in molecule
+  delete(mol);
 
   delete(FileBuffer);