Changeset 9d3264 for src

Timestamp:

Aug 14, 2014, 2:49:51 PM (10 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:

97d6ab, 9e3fca

Parents:

3fbdca

git-author:

Frederik Heber <heber@…> (05/29/14 09:55:28)

git-committer:

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

Message:

Refactored SaturatedFragment::saturate() using list of cut bonds.

• this is preparatory for replacing AddHydrogenReplacementAtom().

File:

• src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) (5 diffs)

src/Fragmentation/Exporters/SaturatedFragment.cpp

@@ -101 +101 @@
 void SaturatedFragment::saturate()
 {
-  // gather all atoms in a vector
+  // so far, we just have a set of keys. Hence, convert to atom refs
+  // and gather all atoms in a vector
   std::vector<atom *> atoms;
   for (KeySet::const_iterator iter = FullMolecule.begin();
@@ -114 +115 @@
 
 //  bool LonelyFlag = false;
+  // go through each atom of the fragment and gather all cut bonds in list
+  typedef std::map<atom *, BondList > CutBonds_t;
+  CutBonds_t CutBonds;
   for (std::vector<atom *>::const_iterator iter = atoms.begin();
       iter != atoms.end();
@@ -125 +129 @@
         ++BondRunner) {
       atom * const OtherWalker = (*BondRunner)->GetOtherAtom(Walker);
-      // if in set
+      // if other atom is in key set
       if (set.find(OtherWalker->getId()) != set.end()) {
         LOG(4, "DEBUG: Walker " << *Walker << " is bound to " << *OtherWalker << ".");
@@ -143 +147 @@
         if (saturation == DoSaturate) {
 //          LOG(3, "ACCEPT: Adding Hydrogen to " << (*iter)->Name << " and a bond in between.");
-          if (!AddHydrogenReplacementAtom(
-              (*BondRunner),
-              Walker,
-              OtherWalker,
-              World::getInstance().getConfig()->IsAngstroem == 1))
-            exit(1);
+          if (CutBonds.count(Walker) == 0)
+            CutBonds.insert( std::make_pair(Walker, BondList() ));
+          CutBonds[Walker].push_back(*BondRunner);
         }
 //        } else if ((treatment == ExcludeHydrogen) && (OtherWalker->getElementNo() == (atomicNumber_t)1)) {
@@ -157 +158 @@
         //NumBonds[(*iter)->getNr()] += Binder->getDegree();
       }
+    }
+  }
+
+  // go through all cut bonds and replace with a hydrogen
+  for (CutBonds_t::const_iterator atomiter = CutBonds.begin();
+      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);
     }
   }