Changeset ea7a50 for src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp

Timestamp:

Feb 22, 2012, 11:26:49 AM (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, Candidate_v1.7.0, 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:

3dfd9c

Parents:

52ed5b

git-author:

Frederik Heber <heber@…> (01/06/12 17:53:45)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:26:49)

Message:

Rewrote some of the descriptors such that they access World's AtomSet and MoleculeSet directly.

• this is the way they are intended. They are friends of the World and may use the sets directly without causing update()s although they return non- const references. This is because here we need not be careful as no atoms are destroyed or added.
• In most cases we had implemented both predicate() and new find() and findAll() that were not necessary (default find..() would do the job better).
• This concerned: AtomOfMoleculeSelectionDescriptor, MoleculeNameDescriptor, MoleculeOfAtomSelectionDescriptor, MoleculeOrderDescriptor, and MoleculePtrDescriptor.
• We left the specific implementation for AtomIdDescriptor and MoleculeIdDescriptor as they directly access World's Atom- and MoleculeSet and may thus find ids significantly faster.
• NOTE: so far some tests are broken and this needs to be fixed yet.

File:

• src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) (3 diffs)

src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp

@@ -43 +43 @@
 
 molecule* MoleculeOfAtomSelectionDescriptor_impl::find(){
-  World &instance = World::getInstance();
-  for (World::AtomSelectionIterator iter = instance.beginAtomSelection();
-      iter != instance.endAtomSelection();
+  World::AtomSet &set = getSelectedAtoms();
+  for (World::AtomSet::internal_iterator iter = set.begin_internal();
+      iter != set.end_internal();
       ++iter) {
-    if (iter->second->getMolecule() != NULL)
+    if (iter->second->getMolecule())
       return iter->second->getMolecule();
   }
@@ -57 +57 @@
   std::set<molecule*> temp;
   std::pair< std::set<molecule*>::iterator, bool> inserter;
-  World &instance = World::getInstance();
-  for (World::AtomSelectionIterator iter = instance.beginAtomSelection();
-      iter != instance.endAtomSelection();
+  World::AtomSet &set = getSelectedAtoms();
+  for (World::AtomSet::internal_iterator iter = set.begin_internal();
+      iter != set.end_internal();
       ++iter) {
-    if (iter->second->getMolecule() != NULL) {
+    if (iter->second->getMolecule()) {
       inserter = temp.insert( iter->second->getMolecule() );
       if (inserter.second)
@@ -70 +70 @@
 }
 
+World::AtomSet& MoleculeOfAtomSelectionDescriptor_impl::getSelectedAtoms(){
+  return World::getInstance().selectedAtoms;
+}
+
 MoleculeDescriptor MoleculesByAtomSelection(){
   return MoleculeDescriptor(MoleculeDescriptor::impl_ptr(new MoleculeOfAtomSelectionDescriptor_impl()));