Changeset de2cbf for src/Fragmentation/Exporters/SaturatedFragment.cpp

Timestamp:

Aug 14, 2014, 2:49:51 PM (11 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:

fec597

Parents:

9e3fca

git-author:

Frederik Heber <heber@…> (05/29/14 10:00:26)

git-committer:

Frederik Heber <heber@…> (08/14/14 14:49:51)

Message:

Added SaturateFragment()::saturateAtom() replacing all cut bonds at once.

• so far, we have just outsourced the loop over each cut bond into this function.

File:

• src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) (1 diff)

src/Fragmentation/Exporters/SaturatedFragment.cpp

@@ -165 +165 @@
       atomiter != CutBonds.end(); ++atomiter) {
     atom * const Walker = atomiter->first;
-    // go through each bond and replace
-    for (BondList::const_iterator bonditer = atomiter->second.begin();
-        bonditer != atomiter->second.end(); ++bonditer) {
-      atom * const OtherWalker = (*bonditer)->GetOtherAtom(Walker);
-      if (!AddHydrogenReplacementAtom(
-          (*bonditer),
-          Walker,
-          OtherWalker,
-          World::getInstance().getConfig()->IsAngstroem == 1))
-        exit(1);
-    }
-  }
+    if (!saturateAtom(Walker, atomiter->second))
+      exit(1);
+  }
+}
+
+bool SaturatedFragment::saturateAtom(
+    atom * const _atom,
+    const BondList &_cutbonds)
+{
+  // go through each bond and replace
+  for (BondList::const_iterator bonditer = _cutbonds.begin();
+      bonditer != _cutbonds.end(); ++bonditer) {
+    atom * const OtherWalker = (*bonditer)->GetOtherAtom(_atom);
+    if (!AddHydrogenReplacementAtom(
+        (*bonditer),
+        _atom,
+        OtherWalker,
+        World::getInstance().getConfig()->IsAngstroem == 1))
+      return false;
+  }
+  return true;
 }