Changeset 07a47e for src/Graph/BreadthFirstSearchAdd.cpp

Timestamp:

Oct 26, 2011, 3:02:53 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:

41d023

Parents:

99b0dc

Message:

Replaced enable/disable-hydrogen by internal switch.

• changes in Fragmentation, Graph and molecule structures.
• switch is now enum HydrogenSaturation that is constant everywhere except in the Actions. FragmentMoleculeAction and DepthFirstSearchAction have new parameter DoSaturation with default value of true.

File:

• src/Graph/BreadthFirstSearchAdd.cpp (modified) (3 diffs)

src/Graph/BreadthFirstSearchAdd.cpp

@@ -32 +32 @@
 
 
-BreadthFirstSearchAdd::BreadthFirstSearchAdd(atom *&_Root, int _BondOrder, bool _IsAngstroem) :
+BreadthFirstSearchAdd::BreadthFirstSearchAdd(atom *&_Root, int _BondOrder, bool _IsAngstroem, const enum HydrogenSaturation _saturation) :
   BondOrder(_BondOrder),
   Root(_Root),
+  saturation(_saturation),
   IsAngstroem(_IsAngstroem)
 {
@@ -100 +101 @@
         AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
       } else {
-#ifdef ADDHYDROGEN
-        if (!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
-        exit(1);
-#endif
+        if (saturation == DoSaturate)
+          if (!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
+            exit(1);
       }
     }
@@ -118 +118 @@
       AddedBondList[Binder] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
     } else { // if it's root bond it has to broken (otherwise we would not create the fragments)
-#ifdef ADDHYDROGEN
-      if(!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
-      exit(1);
-#endif
+      if (saturation == DoSaturate)
+        if(!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
+          exit(1);
     }
   }