Changeset c8302f3 for src/molecule.cpp

Timestamp:

Feb 13, 2013, 2:29:35 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:

7d82a5

Parents:

88c8ec

git-author:

Frederik Heber <heber@…> (11/02/12 13:36:49)

git-committer:

Frederik Heber <heber@…> (02/13/13 14:29:35)

Message:

Removed molecule::RemoveBond(s) and ::removeAtom().

• this functionality has only been used in ListOfBondsUnitTest but nowhere else and it obstructed with change to boost::shared_ptr.

File:

• src/molecule.cpp (modified) (2 diffs)

src/molecule.cpp

@@ -716 +716 @@
 };
 
-/** Remove bond from bond chain list and from the both atom::ListOfBonds.
- * Bond::~Bond takes care of bond removal
- * \param *pointer bond pointer
- * \return true - bound found and removed, false - bond not found/removed
- */
-bool molecule::RemoveBond(bond::ptr pointer)
-{
-  //ELOG(1, "molecule::RemoveBond: Function not implemented yet.");
-  delete(pointer);
-  return true;
-};
-
-/** Remove every bond from bond chain list that atom \a *BondPartner is a constituent of.
- * \todo Function not implemented yet
- * \param *BondPartner atom to be removed
- * \return true - bounds found and removed, false - bonds not found/removed
- */
-bool molecule::RemoveBonds(atom *BondPartner)
-{
-  //ELOG(1, "molecule::RemoveBond: Function not implemented yet.");
-  BondPartner->removeAllBonds();
-  return false;
-};
-
 /** Set molecule::name from the basename without suffix in the given \a *filename.
  * \param *filename filename
@@ -771 +747 @@
     domain.at(i,i) = dim->at(i);
   World::getInstance().setDomain(domain);
-};
-
-/** Removes atom from molecule list and removes all of its bonds.
- * \param *pointer atom to be removed
- * \return true - succeeded, false - atom not found in list
- */
-bool molecule::RemoveAtom(atom *pointer)
-{
-  ASSERT(pointer, "Null pointer passed to molecule::RemoveAtom().");
-  RemoveBonds(pointer);
-  pointer->removeFromMolecule();
-  return true;
 };