Changeset 8e1f901 for src/molecule.cpp

Timestamp:

Mar 30, 2012, 9:16:31 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:

c67ff9

Parents:

5e6534

git-author:

Frederik Heber <heber@…> (03/21/12 11:41:02)

git-committer:

Frederik Heber <heber@…> (03/30/12 09:16:31)

Message:

molecule uses AtomIdSet now, rename getAtoms -> getAtomIds().

• molecule now relies on AtomIdSet functions, only insert() and erase() have own functionality to set the molecule internal id and the atom name.
• FIX: removed MoleculeDescriptor include, added to Fragmentation and DepthFirstSearchAnalysis.

File:

• src/molecule.cpp (modified) (4 diffs)

src/molecule.cpp

@@ -165 +165 @@
 /************************** Access to the List of Atoms ****************/
 
-
-molecule::iterator molecule::begin(){
-  return iterator(atomIds.begin(), FromIdToAtom());
-}
-
-molecule::const_iterator molecule::begin() const{
-  return const_iterator(atomIds.begin(), FromIdToAtom());
-}
-
-molecule::iterator molecule::end(){
-  return iterator(atomIds.end(), FromIdToAtom());
-}
-
-molecule::const_iterator molecule::end() const{
-  return const_iterator(atomIds.end(), FromIdToAtom());
-}
-
-bool molecule::empty() const
-{
-  return (atomIds.empty());
-}
-
-size_t molecule::size() const
-{
-  size_t counter = 0;
-  for (const_iterator iter = begin(); iter != end (); ++iter)
-    counter++;
-  return counter;
-}
-
 molecule::const_iterator molecule::erase( const_iterator loc )
 {
@@ -222 +192 @@
 }
 
-molecule::const_iterator molecule::find ( atom * key ) const
-{
-  return const_iterator(atomIds.find(key->getId()), FromIdToAtom());
-}
-
 pair<molecule::iterator,bool> molecule::insert ( atom * const key )
 {
   OBSERVE;
-  pair<atomIdSet::iterator,bool> res = atomIds.insert(key->getId());
+  std::pair<iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
     key->setNr(atomIdPool.getNextId());
     setAtomName(key);
     formula+=key->getType();
-    return pair<iterator,bool>(iterator(res.first, FromIdToAtom()),res.second);
+    return res;
   } else {
     return pair<iterator,bool>(end(),res.second);
@@ -256 +221 @@
 {
   World::AtomComposite vector_of_atoms;
-//  std::copy(MyIter(atomIds.begin(), FromIdToAtom()),
-//      MyIter(atomIds.end(), FromIdToAtom()),
-//      vector_of_atoms.begin());
-//  for (MyIter iter = MyIter(atomIds.begin(), FromIdToAtom());
-//      iter != MyIter(atomIds.end(), FromIdToAtom());
-//      ++iter)
   for (molecule::iterator iter = begin(); iter != end(); ++iter)
     vector_of_atoms.push_back(*iter);
@@ -851 +810 @@
       "molecule::isInMolecule() - atom is not designated to be in molecule '"
       +toString(this->getName())+"'.");
-  molecule::atomIdSet::const_iterator iter = atomIds.find(_atom->getId());
+  molecule::const_iterator iter = atomIds.find(_atom->getId());
   return (iter != atomIds.end());
 }