Changeset 48d43f for src

Timestamp:

Feb 4, 2011, 6:56:38 PM (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:

a947e9

Parents:

4c2643

git-author:

Frederik Heber <heber@…> (02/02/11 09:51:29)

git-committer:

Frederik Heber <heber@…> (02/04/11 18:56:38)

Message:

molecule::FragmentMolecule() - Bond degree is now re-calculated by default.

• if we load bond graph from file (e.g. pdb), bond degree is not given and set to 1 by default which may not be correct. As bond degree is very important to the fragmentation, we rather re-calculate it before fragmenting.

File:

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

src/molecule_fragmentation.cpp

@@ -661 +661 @@
   FragmentationToDo = FragmentationToDo && CheckAdjacencyFileAgainstMolecule(prefix, ListOfAtoms);
   delete[](ListOfAtoms);
+
+  // === reset bond degree and perform CorrectBondDegree ===
+  for(World::MoleculeIterator iter = World::getInstance().getMoleculeIter();
+      iter != World::getInstance().moleculeEnd();
+      ++iter) {
+      // reset bond degree to 1
+    for (molecule::iterator atomiter = (*iter)->begin();
+        atomiter != (*iter)->end();
+        ++atomiter) {
+      for (BondList::iterator bonditer = (*atomiter)->ListOfBonds.begin();
+          bonditer != (*atomiter)->ListOfBonds.end();
+          ++bonditer) {
+        (*bonditer)->BondDegree = 1;
+      }
+    }
+    // correct bond degree
+    (*iter)->CorrectBondDegree();
+  }
 
   // ===== 2. perform a DFS analysis to gather info on cyclic structure and a list of disconnected subgraphs =====