Changeset 1f693d for src/Fragmentation/Exporters

Timestamp:

Apr 17, 2013, 6:56:54 PM (12 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:

2d5137

Parents:

88ada9

git-author:

Frederik Heber <heber@…> (03/19/13 08:40:28)

git-committer:

Frederik Heber <heber@…> (04/17/13 18:56:54)

Message:

Wrapped Bond::BondDegree in getter.

• This is preparatory for a new signal DegreeChanged.

Location:

src/Fragmentation/Exporters

Files:

• ExportGraph.cpp (modified) (2 diffs)
• SaturatedFragment.cpp (modified) (5 diffs)

src/Fragmentation/Exporters/ExportGraph.cpp

@@ -227 +227 @@
             std::stringstream output;
 //            output << "ACCEPT: Adding Bond: "
-            output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->BondDegree);
+            output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->getDegree());
 //            LOG(3, output.str());
             //NumBonds[(*iter)->getNr()]++;
@@ -244 +244 @@
             // just copy the atom if it's a hydrogen
             atom * const OtherWalker = Leaf->AddCopyAtom(OtherFather);
-            Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->BondDegree);
+            Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
           }
-          //NumBonds[(*iter)->getNr()] += Binder->BondDegree;
+          //NumBonds[(*iter)->getNr()] += Binder->getDegree();
         }
       }

src/Fragmentation/Exporters/SaturatedFragment.cpp

@@ -130 +130 @@
 ////          std::stringstream output;
 ////            output << "ACCEPT: Adding Bond: "
-//          output << Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->BondDegree);
+//          output << Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
 ////            LOG(3, output.str());
 //          //NumBonds[(*iter)->getNr()]++;
@@ -152 +152 @@
 //          // just copy the atom if it's a hydrogen
 //          atom * const OtherWalker = Leaf->AddCopyAtom(OtherWalker);
-//          Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->BondDegree);
+//          Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
 //        }
-        //NumBonds[(*iter)->getNr()] += Binder->BondDegree;
+        //NumBonds[(*iter)->getNr()] += Binder->getDegree();
       }
     }
@@ -266 +266 @@
   ASSERT(Origin->getType() != NULL,
       "SaturatedFragment::AddHydrogenReplacementAtom() - element of Origin is not given.");
-  BondRescale = Origin->getType()->getHBondDistance(TopBond->BondDegree-1);
+  BondRescale = Origin->getType()->getHBondDistance(TopBond->getDegree()-1);
   if (BondRescale == -1) {
-    ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->BondDegree << "!");
+    ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->getDegree() << "!");
     return false;
     BondRescale = bondlength;
@@ -277 +277 @@
 
   // discern single, double and triple bonds
-  switch(TopBond->BondDegree) {
+  switch(TopBond->getDegree()) {
     case 1:
       // check whether replacement has been an excluded hydrogen
@@ -343 +343 @@
       bondangle = Origin->getType()->getHBondAngle(1);
       if (bondangle == -1) {
-        ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->BondDegree << "!");
+        ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->getDegree() << "!");
         return false;
         bondangle = 0;