Changeset c26617 for src/Atom

Timestamp:

Feb 10, 2015, 2:09:08 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:

c1d837

Parents:

e23fec

git-author:

Frederik Heber <heber@…> (01/25/15 12:37:44)

git-committer:

Frederik Heber <heber@…> (02/10/15 14:09:08)

Message:

Undoing atom/molecule removal will also recreate bonds.

• TESTFIX: Molecule/Remove Undo had wrong check file (bonds were still missing)

Location:

src/Atom

Files:

• AtomicInfo.cpp (modified) (3 diffs)
• AtomicInfo.hpp (modified) (2 diffs)

src/Atom/AtomicInfo.cpp

@@ -34 +34 @@
 
 #include "CodePatterns/MemDebug.hpp"
+
+#include "CodePatterns/Log.hpp"
 
 #include "atom.hpp"
@@ -71 +73 @@
       "Atom "+toString(_atom.getId())+" is not associated with any molecule.");
   MolId = mol->getId();
+  // accumulate bond info
+  const BondList &ListOfBonds = _atom.getListOfBonds();
+  bonds.reserve(ListOfBonds.size());
+  for (BondList::const_iterator bonditer = ListOfBonds.begin();
+      bonditer != ListOfBonds.end(); ++bonditer) {
+    const BondInfo bondinfo(*bonditer);
+    bonds.push_back(bondinfo);
+    LOG(3, "DEBUG: Storing info for bond " << bondinfo.leftid << "<->" << bondinfo.rightid);
+  }
 }
 
@@ -101 +112 @@
     }
 
+    // set bonds
+    for (std::vector<BondInfo>::const_iterator bonditer = bonds.begin();
+        bonditer != bonds.end(); ++bonditer)
+      (*bonditer).RecreateBond();
+
     // setting molecule
     molecule * const _mol = World::getInstance().getMolecule(MoleculeById(MolId));

src/Atom/AtomicInfo.hpp

@@ -16 +16 @@
 #include "LinearAlgebra/Vector.hpp"
 #include "types.hpp"
+
+#include <vector>
+
+#include "Bond/BondInfo.hpp"
 
 class atom;
@@ -45 +49 @@
   atomId_t Id;
   int Nr;
+  std::vector<BondInfo> bonds;
 };