Changeset 8e1f901

Timestamp:

Mar 30, 2012, 9:16:31 AM (13 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:

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.

Location:

src

Files:

• Fragmentation/Fragmentation.cpp (modified) (1 diff)
• Graph/DepthFirstSearchAnalysis.cpp (modified) (1 diff)
• molecule.cpp (modified) (4 diffs)
• molecule.hpp (modified) (7 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -27 +27 @@
 #include "Atom/atom.hpp"
 #include "Bond/bond.hpp"
+#include "Descriptors/MoleculeDescriptor.hpp"
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"

src/Graph/DepthFirstSearchAnalysis.cpp

@@ -32 +32 @@
 #include "CodePatterns/Verbose.hpp"
 #include "Descriptors/AtomDescriptor.hpp"
+#include "Descriptors/MoleculeDescriptor.hpp"
 #include "molecule.hpp"
 #include "MoleculeLeafClass.hpp"

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());
 }

src/molecule.hpp

@@ -21 +21 @@
 #include <vector>
 
-#include <boost/iterator/transform_iterator.hpp>
-
 #include <string>
 
+#include "AtomIdSet.hpp"
 #include "Atom/AtomSet.hpp"
 #include "CodePatterns/Cacheable.hpp"
 #include "CodePatterns/Observer/Observable.hpp"
-#include "CodePatterns/Observer/ObservedIterator.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
@@ -36 +34 @@
 #include "IdPool.hpp"
 #include "types.hpp"
-
-// TODO: Was is the include of MoleculeDescriptor_impl.hpp doing in molecule.hpp
-#include "Descriptors/MoleculeDescriptor_impl.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -59 +54 @@
 class Shape;
 
-/******************************** Some definitions for easier reading **********************************/
-
-struct FromIdToAtom :
-  public std::unary_function<atom *, atomId_t>
-{
-    atom * operator()(atomId_t id) const {
-     return World::getInstance().getAtom(AtomById(id));
-    }
-};
-
 /************************************* Class definitions ****************************************/
 
@@ -80 +65 @@
 
 public:
-  typedef std::set<atomId_t> atomIdSet;
-  typedef boost::transform_iterator<FromIdToAtom, atomIdSet::iterator, atom *, atomId_t> iterator;
-  typedef boost::transform_iterator<FromIdToAtom, atomIdSet::const_iterator, const atom *, atomId_t const &> const_iterator;
+  typedef AtomIdSet::atomIdSet atomIdSet;
+  typedef AtomIdSet::iterator iterator;
+  typedef AtomIdSet::const_iterator const_iterator;
 
   int MDSteps; //!< The number of MD steps in Trajectories
@@ -97 +82 @@
   Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
   moleculeId_t id;
-  atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
+  AtomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
   IdPool<atomId_t, uniqueId> atomIdPool;  //!< pool of internal ids such that way may guarantee uniqueness
 
@@ -125 +110 @@
   World::AtomComposite getAtomSet() const;
 
-  iterator begin();
-  const_iterator begin() const;
-  iterator end();
-  const_iterator end() const;
-  bool empty() const;
-  size_t size() const;
-  const_iterator find(atom * key) const;
-  pair<iterator, bool> insert(atom * const key);
+  // simply pass on all functions to AtomIdSet
+  iterator begin() {
+    return atomIds.begin();
+  }
+  const_iterator begin() const
+  {
+    return atomIds.begin();
+  }
+  iterator end()
+  {
+    return atomIds.end();
+  }
+  const_iterator end() const
+  {
+    return atomIds.end();
+  }
+  bool empty() const
+  {
+    return atomIds.empty();
+  }
+  size_t size() const
+  {
+    return atomIds.size();
+  }
+  const_iterator find(atom * key) const
+  {
+    return atomIds.find(key);
+  }
+  const atomIdSet & getAtomIds() const {
+    return atomIds.getAtomIds();
+  }
+
+  std::pair<iterator, bool> insert(atom * const key);
+
   bool containsAtom(atom* key);
 
@@ -145 +156 @@
    */
   const_iterator erase(const_iterator loc);
+
   /** Erase an atom from the list.
    * \note This should only be called by atom::removeFromMolecule(),