Changeset 401f90 for src

Timestamp:

Dec 28, 2011, 3:27:15 PM (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:

3e4fb6

Parents:

f9b967 (diff), adb5cda (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Removing_molecule_atomSet' into Merge_molecule_atomSet_removal

Conflicts:

src/molecule_geometry.cpp

• molecule::CenterInBox(): don't use BOOST_FOREACH but new transform_iterators.

Location:

src

Files:

• Actions/WorldAction/BoundInBoxAction.cpp (modified) (1 diff)
• Actions/WorldAction/CenterInBoxAction.cpp (modified) (1 diff)
• Analysis/analysis_correlation.cpp (modified) (7 diffs)
• Analysis/analysis_correlation.hpp (modified) (1 diff)
• Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) (1 diff)
• Dynamics/LinearInterpolationBetweenSteps.hpp (modified) (1 diff)
• Dynamics/MinimiseConstrainedPotential.cpp (modified) (14 diffs)
• Dynamics/MinimiseConstrainedPotential.hpp (modified) (3 diffs)
• Dynamics/VerletForceIntegration.hpp (modified) (1 diff)
• Fragmentation/Fragmentation.cpp (modified) (2 diffs)
• Graph/BuildInducedSubgraph.cpp (modified) (2 diffs)
• MoleculeLeafClass.cpp (modified) (2 diffs)
• Parser/FormatParserStorage.cpp (modified) (2 diffs)
• Tesselation/BoundaryMaps.hpp (modified) (1 diff)
• Tesselation/boundary.cpp (modified) (2 diffs)
• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• molecule.cpp (modified) (16 diffs)
• molecule.hpp (modified) (6 diffs)
• molecule_geometry.cpp (modified) (17 diffs)
• molecule_graph.cpp (modified) (4 diffs)
• moleculelist.cpp (modified) (1 diff)

src/Actions/WorldAction/BoundInBoxAction.cpp

@@ -76 +76 @@
       MolRunner != AllMolecules.end();
       ++MolRunner) {
-    for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
+    for(molecule::iterator AtomRunner = (*MolRunner)->begin();
         AtomRunner != (*MolRunner)->end();
         ++AtomRunner) {

src/Actions/WorldAction/CenterInBoxAction.cpp

@@ -109 +109 @@
       MolRunner != AllMolecules.end();
       ++MolRunner) {
-    for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
+    for(molecule::iterator AtomRunner = (*MolRunner)->begin();
         AtomRunner != (*MolRunner)->end();
         ++AtomRunner) {

src/Analysis/analysis_correlation.cpp

@@ -212 +212 @@
     LOG(1,"INFO: Resulting relative angle for molecule " << _mol->getName()
         << " is " << angle << ".");
-    outmap->insert ( make_pair (angle, *iter ) );
+    outmap->insert ( std::make_pair (angle, *iter ) );
     ++i;
   }
@@ -322 +322 @@
                 distance = domain.periodicDistance((*iter)->getPosition(),(*runner)->getPosition());
                 //LOG(1, "Inserting " << *(*iter) << " and " << *(*runner));
-                outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> ((*iter), (*runner)) ) );
+                outmap->insert (
+                    std::pair<double, std::pair <const atom *, const atom*> > (
+                        distance,
+                        std::pair<const atom *, const atom*> ((*iter), (*runner))
+                        )
+                    );
               }
           }
@@ -403 +408 @@
                               distance = checkX.distance(checkOtherX);
                               //LOG(1, "Inserting " << *(*iter) << " and " << *(*runner));
-                              outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> ((*iter), (*runner)) ) );
+                              outmap->insert (
+                                  std::pair<double, std::pair <const atom *, const atom*> > (
+                                      distance,
+                                      std::pair<const atom *, const atom*> (
+                                          (*iter),
+                                          (*runner))
+                                      )
+                                  );
                             }
                       }
@@ -444 +456 @@
           distance = domain.periodicDistance((*iter)->getPosition(),*point);
           LOG(4, "Current distance is " << distance << ".");
-          outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> ((*iter), point) ) );
+          outmap->insert (
+              std::pair<double, std::pair<const atom *, const Vector*> >(
+                  distance,
+                  std::pair<const atom *, const Vector*> (
+                      (*iter),
+                      point)
+                  )
+              );
         }
     }
@@ -491 +510 @@
                 distance = checkX.distance(*point);
                 LOG(4, "Current distance is " << distance << ".");
-                outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (*iter, point) ) );
+                outmap->insert (
+                    std::pair<double,
+                    std::pair<const atom *, const Vector*> >(
+                        distance,
+                        std::pair<const atom *, const Vector*> (
+                            *iter,
+                            point)
+                        )
+                    );
               }
         }
@@ -533 +560 @@
           distance = Intersections.GetSmallestDistance();
           triangle = Intersections.GetClosestTriangle();
-          outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> ((*iter), triangle) ) );
+          outmap->insert (
+              std::pair<double,
+              std::pair<const atom *, BoundaryTriangleSet*> >(
+                  distance,
+                  std::pair<const atom *, BoundaryTriangleSet*> (
+                      (*iter),
+                      triangle)
+                  )
+              );
         }
     }
@@ -597 +632 @@
               }
           // insert
-          outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(ShortestDistance, pair<atom *, BoundaryTriangleSet*> (*iter, ShortestTriangle) ) );
+          outmap->insert (
+              std::pair<double,
+              std::pair<const atom *, BoundaryTriangleSet*> >(
+                  ShortestDistance,
+                  std::pair<const atom *, BoundaryTriangleSet*> (
+                      *iter,
+                      ShortestTriangle)
+                  )
+              );
           //LOG(1, "INFO: Inserting " << Walker << " with distance " << ShortestDistance << " to " << *ShortestTriangle << ".");
         }

src/Analysis/analysis_correlation.hpp

@@ -46 +46 @@
 /********************************************** definitions *********************************/
 
-typedef multimap<double, pair<atom *, atom *> > PairCorrelationMap;
-typedef multimap<double, atom * > DipoleAngularCorrelationMap;
-typedef multimap<double, pair<molecule *, molecule *> > DipoleCorrelationMap;
-typedef multimap<double, pair<atom *, const Vector *> > CorrelationToPointMap;
-typedef multimap<double, pair<atom *, BoundaryTriangleSet *> > CorrelationToSurfaceMap;
+typedef multimap<double, pair<const atom *, const atom *> > PairCorrelationMap;
+typedef multimap<double, const atom * > DipoleAngularCorrelationMap;
+typedef multimap<double, pair<const molecule *, const molecule *> > DipoleCorrelationMap;
+typedef multimap<double, pair<const atom *, const Vector *> > CorrelationToPointMap;
+typedef multimap<double, pair<const atom *, BoundaryTriangleSet *> > CorrelationToSurfaceMap;
 typedef map<double, int> BinPairMap;
 

src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp

@@ -53 +53 @@
       iter != instance.endMoleculeSelection();
       ++iter) {
-    transform(iter->second->begin(),
-              iter->second->end(),
-              back_inserter(res),
-              _take<atom*,molecule::atomSet::value_type>::get);
+    std::copy(iter->second->begin(), iter->second->end(), res.begin());
   }
   return res;

src/Dynamics/LinearInterpolationBetweenSteps.hpp

@@ -55 +55 @@
     if (!MapByIdentity) {
       LOG(1, "STATUS: Constructing atom mapping from start to end position.");
-      molecule::atomSet atoms_list;
-      copy(atoms.begin(), atoms.end(), atoms_list.begin());
-      MinimiseConstrainedPotential Minimiser(atoms_list, PermutationMap);
+      MinimiseConstrainedPotential Minimiser(atoms, PermutationMap);
       Minimiser(startstep, endstep, IsAngstroem);
     } else {

src/Dynamics/MinimiseConstrainedPotential.cpp

@@ -40 +40 @@
 
 MinimiseConstrainedPotential::MinimiseConstrainedPotential(
-    molecule::atomSet &_atoms,
+    World::AtomComposite &_atoms,
     std::map<atom*, atom *> &_PermutationMap) :
   atoms(_atoms),
@@ -59 +59 @@
   PermutationMap.clear();
   DoubleList.clear();
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     DistanceList[*iter].clear();
   }
@@ -90 +90 @@
     LOG(2, "Starting round " << ++round << ", at current potential " << OldPotential << " ... ");
     OlderPotential = OldPotential;
-    molecule::atomSet::const_iterator iter;
+    World::AtomComposite::const_iterator iter;
     do {
       iter = atoms.begin();
@@ -105 +105 @@
         //LOG(2, "Current Walker: " << *(*iter) << " with old/next candidate " << *Sprinter << "/" << *DistanceIterators[(*iter)]->second << ".");
         // find source of the new target
-        molecule::atomSet::const_iterator runner = atoms.begin();
+        World::AtomComposite::const_iterator runner = atoms.begin();
         for (; runner != atoms.end(); ++runner) { // find the source whose toes we might be stepping on (Walker's new target should be in use by another already)
           if (PermutationMap[(*runner)] == DistanceIterators[(*iter)]->second) {
@@ -165 +165 @@
 void MinimiseConstrainedPotential::FillDistanceList()
 {
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
-    for (molecule::atomSet::const_iterator runner = atoms.begin(); runner != atoms.end(); ++runner) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+    for (World::AtomComposite::const_iterator runner = atoms.begin(); runner != atoms.end(); ++runner) {
       DistanceList[(*iter)].insert( DistancePair((*iter)->getPositionAtStep(startstep).distance((*runner)->getPositionAtStep(endstep)), (*runner)) );
     }
@@ -174 +174 @@
 void MinimiseConstrainedPotential::CreateInitialLists()
 {
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     StepList[(*iter)] = DistanceList[(*iter)].begin();    // stores the step to the next iterator that could be a possible next target
     PermutationMap[(*iter)] = DistanceList[(*iter)].begin()->second;   // always pick target with the smallest distance
@@ -185 +185 @@
 void MinimiseConstrainedPotential::MakeInjectivePermutation()
 {
-  molecule::atomSet::const_iterator iter = atoms.begin();
+  World::AtomComposite::const_iterator iter = atoms.begin();
   DistanceMap::iterator NewBase;
   double Potential = fabs(ConstrainedPotential());
@@ -204 +204 @@
     Potential = TryNextNearestNeighbourForInjectivePermutation((*iter), Potential);
   }
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     // now each single entry in the DoubleList should be <=1
     if (DoubleList[*iter] > 1) {
@@ -216 +216 @@
 unsigned int MinimiseConstrainedPotential::CalculateDoubleList()
 {
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
     DoubleList[*iter] = 0;
   unsigned int doubles = 0;
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
       DoubleList[ PermutationMap[*iter] ]++;
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
     if (DoubleList[*iter] > 1)
       doubles++;
@@ -235 +235 @@
   zeile1 << "PermutationMap: ";
   zeile2 << "                ";
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     zeile1 << (*iter)->getName() << " ";
     zeile2 << (PermutationMap[*iter])->getName() << " ";
   }
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     std::map<atom *, unsigned int>::const_iterator value_iter = DoubleList.find(*iter);
     if (value_iter->second > (unsigned int)1)
@@ -255 +255 @@
   // go through every atom
   atom *Runner = NULL;
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     // first term: distance to target
     Runner = PermutationMap[(*iter)];   // find target point
@@ -299 +299 @@
 {
   double result = 0.;
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     if ((PermutationMap[Walker] == PermutationMap[(*iter)]) && (Walker < (*iter))) {
 //    atom *Sprinter = PermutationMap[Walker->nr];
@@ -324 +324 @@
   double Norm1, Norm2, tmp, result = 0.;
 
-  for (molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     if ((*iter) == Walker) // hence, we only go up to the Walker, not beyond (similar to i=0; i<j; i++)
       break;
@@ -407 +407 @@
   /// evaluate forces (only the distance to target dependent part) with the final PermutationMap
   LOG(1, "Calculating forces and adding onto ForceMatrix ... ");
-  for(molecule::atomSet::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for(World::AtomComposite::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
     atom *Sprinter = PermutationMap[(*iter)];
     // set forces

src/Dynamics/MinimiseConstrainedPotential.hpp

@@ -19 +19 @@
 #include <map>
 
-#include "molecule.hpp"
+#include "World.hpp"
 
 /** Structure to contain parameters needed for evaluation of constraint potential.
@@ -33 +33 @@
    * @return
    */
-  MinimiseConstrainedPotential(molecule::atomSet &_atoms, std::map<atom*, atom *> &_PermutationMap);
+  MinimiseConstrainedPotential(World::AtomComposite &_atoms, std::map<atom*, atom *> &_PermutationMap);
 
   /** Destructor.
@@ -79 +79 @@
   typedef std::pair < DistanceMap::iterator, bool> DistanceTestPair;
 
-  molecule::atomSet atoms;
+  World::AtomComposite atoms;
   int startstep; //!< start configuration (MDStep in atom::trajectory)
   int endstep; //!< end configuration (MDStep in atom::trajectory)

src/Dynamics/VerletForceIntegration.hpp

@@ -98 +98 @@
       // calculate forces and potential
       std::map<atom *, atom*> PermutationMap;
-      molecule::atomSet atoms_list;
-      copy(atoms.begin(), atoms.end(), atoms_list.begin());
-      MinimiseConstrainedPotential Minimiser(atoms_list, PermutationMap);
+      MinimiseConstrainedPotential Minimiser(atoms, PermutationMap);
       //double ConstrainedPotentialEnergy =
       Minimiser(DoConstrainedMD, 0, IsAngstroem);

src/Fragmentation/Fragmentation.cpp

@@ -595 +595 @@
 
     // set atom values
-    for(molecule::const_iterator iter=mol->begin();iter!=mol->end();++iter){
+    for(molecule::iterator iter=mol->begin();iter!=mol->end();++iter){
       (*iter)->AdaptiveOrder = OrderArray[(*iter)->getNr()];
       (*iter)->MaxOrder = MaxArray[(*iter)->getNr()];
@@ -676 +676 @@
 
   // we increment the iter just before skipping the hydrogen
-  for (molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end();) {
+  // as we use AddBond, we cannot have a const_iterator here
+  for (molecule::iterator iter = Leaf->begin(); iter != Leaf->end();) {
     LonelyFlag = true;
     FatherOfRunner = (*iter)->father;

src/Graph/BuildInducedSubgraph.cpp

@@ -46 +46 @@
   // fill parent list with sons
   LOG(3, "Filling Parent List.");
-  for (molecule::const_iterator iter = Son->begin(); iter != Son->end(); ++iter) {
+  for (molecule::iterator iter = Son->begin(); iter != Son->end(); ++iter) {
     ParentList[(*iter)->father] = (*iter);
     // Outputting List for debugging
@@ -59 +59 @@
   // check each entry of parent list and if ok (one-to-and-onto matching) create bonds
   LOG(2, "STATUS: Creating bonds.");
-  for (molecule::const_iterator iter = Father->begin(); iter != Father->end(); ++iter) {
+  for (molecule::iterator iter = Father->begin(); iter != Father->end(); ++iter) {
     if (ParentList.count(*iter)) {
       if (ParentList[(*iter)]->father != (*iter)) {

src/MoleculeLeafClass.cpp

@@ -110 +110 @@
 bool MoleculeLeafClass::FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter, const enum HydrogenSaturation saturation)
 {
-  atom *Father = NULL;
-
   if (RootStack != NULL) {
     // find first root candidates
@@ -117 +115 @@
       RootStack[FragmentCounter].clear();
       for(molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ++iter) {
-        Father = (*iter)->GetTrueFather();
+        const atom * const Father = (*iter)->GetTrueFather();
         if (AtomMask[Father->getNr()]) // apply mask
           if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen

src/Parser/FormatParserStorage.cpp

@@ -267 +267 @@
  * We store in the order of the atomic ids, not in the order they appear in the molecules.
  * Hence, we first create a vector from all selected molecules' atoms.
+ *
+ * TODO: Change here atom * to const atom * when FormatParserStorage::save() uses vector<const atom *>
+ *
  * \param &output output stream
  * \param suffix
@@ -278 +281 @@
       MolIter != molecules.end();
       ++MolIter) {
-    for(molecule::atomSet::const_iterator AtomIter = (*MolIter)->begin();
+    for(molecule::iterator AtomIter = (*MolIter)->begin();
         AtomIter != (*MolIter)->end();
         ++AtomIter) {

src/Tesselation/BoundaryMaps.hpp

@@ -29 +29 @@
 
 // ============= TesselPoint maps ======================== //
-typedef std::pair < double, class TesselPoint * > TesselPointDistancePair;
-typedef std::multimap < double, class TesselPoint * > TesselPointDistanceMap;
-typedef std::pair < TesselPointDistanceMap::iterator, bool > TesselPointDistanceTestPair;
+typedef std::pair < double, TesselPoint * > TesselPointDistancePair;
+//typedef std::multimap < double, class TesselPoint * > TesselPointDistanceMap;
+//typedef std::pair < TesselPointDistanceMap::iterator, bool > TesselPointDistanceTestPair;
 
 typedef std::list <TesselPoint *> TesselPointList;

src/Tesselation/boundary.cpp

@@ -189 +189 @@
 
     // 3b. construct set of all points, transformed into cylindrical system and with left and right neighbours
-    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    // Boundaries stores non-const TesselPoint ref, hence we need iterator here
+    for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
       ProjectedVector = (*iter)->getPosition() - (*MolCenter);
       ProjectedVector.ProjectOntoPlane(AxisVector);
@@ -874 +875 @@
             phi[i] = (random()/(rng_max-rng_min))*(2.*M_PI);
 
-        for(molecule::const_iterator iter = filler->begin(); iter !=filler->end();++iter){
+        // atom::clone is not const member function, hence we need iterator here
+        for(molecule::iterator iter = filler->begin(); iter !=filler->end();++iter){
 
           // create atomic random translation vector ...

src/atom.cpp

@@ -79 +79 @@
 
 atom *atom::GetTrueFather()
+{
+  const atom *father = const_cast<const atom *>(this)->GetTrueFather();
+  return const_cast<atom *>(father);
+}
+
+const atom *atom::GetTrueFather() const
 {
   if(father == this){ // top most father is the one that points on itself

src/atom.hpp

@@ -153 +153 @@
    */
   atom *GetTrueFather();
+
+  /** Const version of \sa GetTrueFather().
+   * \return true father, i.e. whose father points to itself, NULL if it could not be found or has none (added hydrogen)
+   */
+  const atom *GetTrueFather() const;
 
   /** Compares the indices of \a this atom with a given \a ptr.

src/molecule.cpp

@@ -150 +150 @@
 
 molecule::iterator molecule::begin(){
-  return molecule::iterator(atoms.begin(),this);
+  return iterator(atomIds.begin(), FromIdToAtom());
 }
 
 molecule::const_iterator molecule::begin() const{
-  return atoms.begin();
+  return const_iterator(atomIds.begin(), FromIdToAtom());
 }
 
 molecule::iterator molecule::end(){
-  return molecule::iterator(atoms.end(),this);
+  return iterator(atomIds.end(), FromIdToAtom());
 }
 
 molecule::const_iterator molecule::end() const{
-  return atoms.end();
+  return const_iterator(atomIds.end(), FromIdToAtom());
 }
 
 bool molecule::empty() const
 {
-  return (begin() == end());
+  return (atomIds.empty());
 }
 
@@ -173 +173 @@
 {
   size_t counter = 0;
-  for (molecule::const_iterator iter = begin(); iter != end (); ++iter)
+  for (const_iterator iter = begin(); iter != end (); ++iter)
     counter++;
   return counter;
@@ -181 +181 @@
 {
   OBSERVE;
-  molecule::const_iterator iter = loc;
-  iter++;
-  atom* atom = *loc;
-  atomIds.erase( atom->getId() );
-  atoms.remove( atom );
-  formula-=atom->getType();
-  atom->removeFromMolecule();
+  const_iterator iter = loc;
+  ++iter;
+  atom * const _atom = const_cast<atom *>(*loc);
+  atomIds.erase( _atom->getId() );
+  formula-=_atom->getType();
+  _atom->removeFromMolecule();
   return iter;
 }
@@ -194 +193 @@
 {
   OBSERVE;
-  molecule::const_iterator iter = find(key);
+  const_iterator iter = find(key);
   if (iter != end()){
-    iter++;
+    ++iter;
     atomIds.erase( key->getId() );
-    atoms.remove( key );
     formula-=key->getType();
     key->removeFromMolecule();
@@ -207 +205 @@
 molecule::const_iterator molecule::find ( atom * key ) const
 {
-  molecule::const_iterator iter;
-  for (molecule::const_iterator Runner = begin(); Runner != end(); ++Runner) {
-    if (*Runner == key)
-      return molecule::const_iterator(Runner);
-  }
-  return molecule::const_iterator(atoms.end());
+  return const_iterator(atomIds.find(key->getId()), FromIdToAtom());
 }
 
@@ -220 +213 @@
   pair<atomIdSet::iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
-    atoms.push_back(key);
     formula+=key->getType();
-    return pair<iterator,bool>(molecule::iterator(--end()),res.second);
+    return pair<iterator,bool>(iterator(res.first, FromIdToAtom()),res.second);
   } else {
-    return pair<iterator,bool>(molecule::iterator(end()),res.second);
+    return pair<iterator,bool>(end(),res.second);
   }
 }
@@ -235 +227 @@
 {
   World::AtomComposite vector_of_atoms;
-  BOOST_FOREACH(atom *_atom, atoms)
-    vector_of_atoms.push_back(_atom);
+//  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);
   return vector_of_atoms;
 }
@@ -635 +633 @@
 
   // copy all atoms
-  for_each(atoms.begin(),atoms.end(),bind1st(mem_fun(&molecule::AddCopyAtom),copy));
+  std::map< const atom *, atom *> FatherFinder;
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    atom * const copy_atom = copy->AddCopyAtom(*iter);
+    FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
+  }
+
+  // copy all bonds
+  for(const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
+    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
+    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
+        BondRunner != ListOfBonds.end();
+        ++BondRunner)
+      if ((*BondRunner)->leftatom == *AtomRunner) {
+        bond *Binder = (*BondRunner);
+        // get the pendant atoms of current bond in the copy molecule
+        ASSERT(FatherFinder.count(Binder->leftatom),
+            "molecule::CopyMolecule() - No copy of original left atom "
+            +toString(Binder->leftatom)+" for bond copy found");
+        ASSERT(FatherFinder.count(Binder->rightatom),
+            "molecule::CopyMolecule() - No copy of original right atom "
+            +toString(Binder->rightatom)+"  for bond copy found");
+        atom * const LeftAtom = FatherFinder[Binder->leftatom];
+        atom * const RightAtom = FatherFinder[Binder->rightatom];
+
+        bond * const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
+        NewBond->Cyclic = Binder->Cyclic;
+        if (Binder->Cyclic)
+          copy->NoCyclicBonds++;
+        NewBond->Type = Binder->Type;
+      }
+  }
+  // correct fathers
+  //for_each(begin(),end(),mem_fun(&atom::CorrectFather));
+
+  return copy;
+};
+
+
+/** Destroys all atoms inside this molecule.
+ */
+void molecule::removeAtomsinMolecule()
+{
+  // remove each atom from world
+  for(iterator AtomRunner = begin(); !empty(); AtomRunner = begin())
+    World::getInstance().destroyAtom(*AtomRunner);
+};
+
+
+/**
+ * Copies all atoms of a molecule which are within the defined parallelepiped.
+ *
+ * @param offest for the origin of the parallelepiped
+ * @param three vectors forming the matrix that defines the shape of the parallelpiped
+ */
+molecule* molecule::CopyMoleculeFromSubRegion(const Shape &region) const {
+  molecule *copy = World::getInstance().createMolecule();
+
+  // copy all atoms
+  std::map< const atom *, atom *> FatherFinder;
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    if((*iter)->IsInShape(region)){
+      atom * const copy_atom = copy->AddCopyAtom(*iter);
+      FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
+    }
+  }
 
   // copy all bonds
@@ -645 +707 @@
       if ((*BondRunner)->leftatom == *AtomRunner) {
         bond *Binder = (*BondRunner);
-        // get the pendant atoms of current bond in the copy molecule
-        atomSet::iterator leftiter=find_if(copy->atoms.begin(),copy->atoms.end(),bind2nd(mem_fun(&atom::isFather),Binder->leftatom));
-        atomSet::iterator rightiter=find_if(copy->atoms.begin(),copy->atoms.end(),bind2nd(mem_fun(&atom::isFather),Binder->rightatom));
-        ASSERT(leftiter!=copy->atoms.end(),"No copy of original left atom for bond copy found");
-        ASSERT(leftiter!=copy->atoms.end(),"No copy of original right atom for bond copy found");
-        atom *LeftAtom = *leftiter;
-        atom *RightAtom = *rightiter;
-
-        bond *NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
-        NewBond->Cyclic = Binder->Cyclic;
-        if (Binder->Cyclic)
-          copy->NoCyclicBonds++;
-        NewBond->Type = Binder->Type;
+        if ((FatherFinder.count(Binder->leftatom))
+            && (FatherFinder.count(Binder->rightatom))) {
+          // if copy present, then it must be from subregion
+          atom * const LeftAtom = FatherFinder[Binder->leftatom];
+          atom * const RightAtom = FatherFinder[Binder->rightatom];
+
+          bond * const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
+          NewBond->Cyclic = Binder->Cyclic;
+          if (Binder->Cyclic)
+            copy->NoCyclicBonds++;
+          NewBond->Type = Binder->Type;
+        }
       }
   }
   // correct fathers
-  //for_each(atoms.begin(),atoms.end(),mem_fun(&atom::CorrectFather));
-
-  return copy;
-};
-
-
-/** Destroys all atoms inside this molecule.
- */
-void molecule::removeAtomsinMolecule()
-{
-  // remove each atom from world
-  for(molecule::const_iterator AtomRunner = begin(); !empty(); AtomRunner = begin())
-    World::getInstance().destroyAtom(*AtomRunner);
-};
-
-
-/**
- * Copies all atoms of a molecule which are within the defined parallelepiped.
- *
- * @param offest for the origin of the parallelepiped
- * @param three vectors forming the matrix that defines the shape of the parallelpiped
- */
-molecule* molecule::CopyMoleculeFromSubRegion(const Shape &region) const {
-  molecule *copy = World::getInstance().createMolecule();
-
-  BOOST_FOREACH(atom *iter,atoms){
-    if(iter->IsInShape(region)){
-      copy->AddCopyAtom(iter);
-    }
-  }
+  //for_each(begin(),end(),mem_fun(&atom::CorrectFather));
 
   //TODO: copy->BuildInducedSubgraph(this);
@@ -709 +741 @@
 
   // some checks to make sure we are able to create the bond
-  ASSERT(atom1, "First atom in bond-creation was an invalid pointer");
-  ASSERT(atom2, "Second atom in bond-creation was an invalid pointer");
-  ASSERT(FindAtom(atom1->getNr()),"First atom in bond-creation was not part of molecule");
-  ASSERT(FindAtom(atom2->getNr()),"Second atom in bond-creation was not part of molecule");
+  ASSERT(atom1,
+      "molecule::AddBond() - First atom "+toString(atom1)
+      +" is not a invalid pointer");
+  ASSERT(atom2,
+      "molecule::AddBond() - Second atom "+toString(atom2)
+      +" is not a invalid pointer");
+  ASSERT(isInMolecule(atom1),
+      "molecule::AddBond() - First atom "+toString(atom1)
+      +" is not part of molecule");
+  ASSERT(isInMolecule(atom2),
+      "molecule::AddBond() - Second atom "+toString(atom2)
+      +" is not part of molecule");
 
   Binder = new bond(atom1, atom2, degree);
   atom1->RegisterBond(WorldTime::getTime(), Binder);
   atom2->RegisterBond(WorldTime::getTime(), Binder);
-  if ((atom1->getType() != NULL) && (atom1->getType()->getAtomicNumber() != 1) && (atom2->getType() != NULL) && (atom2->getType()->getAtomicNumber() != 1))
+  if ((atom1->getType() != NULL)
+      && (atom1->getType()->getAtomicNumber() != 1)
+      && (atom2->getType() != NULL)
+      && (atom2->getType()->getAtomicNumber() != 1))
     NoNonBonds++;
 
@@ -820 +863 @@
 atom * molecule::FindAtom(int Nr)  const
 {
-  molecule::const_iterator iter = begin();
+  molecule::iterator iter = begin();
   for (; iter != end(); ++iter)
-    if ((*iter)->getNr() == Nr)
-      break;
+  if ((*iter)->getNr() == Nr)
+    break;
   if (iter != end()) {
     //LOG(0, "Found Atom Nr. " << walker->getNr());
     return (*iter);
   } else {
-    LOG(0, "Atom not found in list.");
+    ELOG(1, "Atom not found in molecule " << getName() << "'s list.");
     return NULL;
   }
-};
+}
+
+/** Checks whether the given atom is a member of this molecule.
+ *
+ *  We make use here of molecule::atomIds to get a result on
+ *
+ * @param _atom atom to check
+ * @return true - is member, false - is not
+ */
+bool molecule::isInMolecule(const atom * const _atom)
+{
+  ASSERT(_atom->getMolecule() == this,
+      "molecule::isInMolecule() - atom is not designated to be in molecule '"
+      +toString(this->getName())+"'.");
+  molecule::atomIdSet::const_iterator iter = atomIds.find(_atom->getId());
+  return (iter != atomIds.end());
+}
 
 /** Asks for atom number, and checks whether in list.
@@ -878 +937 @@
     enumeration<const element*> elementLookup = formula.enumerateElements();
     *output << "#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)" << endl;
-    for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputArrayIndexed,_1,output,elementLookup,AtomNo,(const char*)0));
+    for_each(begin(),end(),boost::bind(&atom::OutputArrayIndexed,_1,output,elementLookup,AtomNo,(const char*)0));
     return true;
   }
@@ -900 +959 @@
       memset(AtomNo,0,(MAX_ELEMENTS-1)*sizeof(*AtomNo));
       enumeration<const element*> elementLookup = formula.enumerateElements();
-      for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputTrajectory,_1,output,elementLookup, AtomNo, (const int)step));
+      for_each(begin(),end(),boost::bind(&atom::OutputTrajectory,_1,output,elementLookup, AtomNo, (const int)step));
     }
     return true;
@@ -941 +1000 @@
     for (int step=0;step<MDSteps;step++) {
       *output << getAtomCount() << "\n\tCreated by molecuilder, step " << step << ", on " << ctime(&now);
-      for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputTrajectoryXYZ,_1,output,step));
+      for_each(begin(),end(),boost::bind(&atom::OutputTrajectoryXYZ,_1,output,step));
     }
     return true;
@@ -958 +1017 @@
     now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
     *output << getAtomCount() << "\n\tCreated by molecuilder on " << ctime(&now);
-    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputXYZLine),output));
+    for_each(begin(),end(),bind2nd(mem_fun(&atom::OutputXYZLine),output));
     return true;
   } else
@@ -972 +1031 @@
   int i = 0;
   NoNonHydrogen = 0;
-  for (molecule::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+  for (molecule::iterator iter = begin(); iter != end(); ++iter) {
     (*iter)->setNr(i);   // update number in molecule (for easier referencing in FragmentMolecule lateron)
     if ((*iter)->getType()->getAtomicNumber() != 1) // count non-hydrogen atoms whilst at it

src/molecule.hpp

@@ -21 +21 @@
 #include <vector>
 
+#include <boost/iterator/transform_iterator.hpp>
+
 #include <string>
 
-#include "types.hpp"
+#include "AtomSet.hpp"
 #include "CodePatterns/Observer.hpp"
 #include "CodePatterns/ObservedIterator.hpp"
 #include "CodePatterns/Cacheable.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
+#include "Formula.hpp"
 #include "Helpers/defs.hpp"
-#include "Formula.hpp"
-#include "AtomSet.hpp"
-
+#include "types.hpp"
+
+// TODO: Was is the include of MoleculeDescriptor_impl.hpp doing in molecule.hpp
 #include "Descriptors/MoleculeDescriptor_impl.hpp"
 
@@ -55 +59 @@
 /******************************** 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 ****************************************/
 
@@ -66 +78 @@
 
 public:
-  typedef ATOMSET(std::list) atomSet;
   typedef std::set<atomId_t> atomIdSet;
-  typedef ObservedIterator<atomSet> iterator;
-  typedef atomSet::const_iterator const_iterator;
+  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;
 
   const periodentafel * const elemente; //!< periodic table with each element
-  // old deprecated atom handling
-  //atom *start;        //!< start of atom list
-  //atom *end;          //!< end of atom list
-  //bond *first;        //!< start of bond list
-  //bond *last;         //!< end of bond list
   int MDSteps; //!< The number of MD steps in Trajectories
   mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
@@ -82 +88 @@
   mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
   bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
-  //Vector Center;      //!< Center of molecule in a global box
   int IndexNr; //!< index of molecule in a MoleculeListClass
   char name[MAXSTRINGSIZE]; //!< arbitrary name
@@ -91 +96 @@
   Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
   moleculeId_t id;
-  atomSet atoms; //<!list of atoms
   atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
 protected:
-  //void CountAtoms();
-  /**
-   * this iterator type should be used for internal variables, \
-     * since it will not lock
-   */
-  typedef atomSet::iterator internal_iterator;
 
   molecule(const periodentafel * const teil);
@@ -174 +172 @@
   atom * FindAtom(int Nr) const;
   atom * AskAtom(string text);
+  bool isInMolecule(const atom * const _atom);
 
   /// Count and change present atoms' coordination.

src/molecule_geometry.cpp

@@ -55 +55 @@
 
   // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
+  for (iterator iter = begin(); iter != end(); ++iter) {
     if (DoLog(4) && (*Center != *CenterBox))
-      LOG(4, "INFO: atom before is at " << *iter);
-    *iter -= *Center;
-    *iter += *CenterBox;
+      LOG(4, "INFO: atom before is at " << **iter);
+    **iter -= *Center;
+    **iter += *CenterBox;
     if (DoLog(4) && (*Center != *CenterBox))
-      LOG(4, "INFO: atom after is at " << *iter);
-  }
-  atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
+      LOG(4, "INFO: atom after is at " << **iter);
+  }
+  getAtomSet().transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
 
   delete(Center);
@@ -80 +80 @@
 
   // go through all atoms
-  atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
+  getAtomSet().transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
 
   return status;
@@ -94 +94 @@
   Vector *min = new Vector;
 
-  molecule::const_iterator iter = begin();  // start at first in list
+  const_iterator iter = begin();  // start at first in list
   if (iter != end()) { //list not empty?
     for (int i=NDIM;i--;) {
@@ -122 +122 @@
 {
   int Num = 0;
-  molecule::const_iterator iter = begin();  // start at first in list
+  const_iterator iter = begin();  // start at first in list
   Vector Center;
 
@@ -141 +141 @@
 Vector * molecule::DetermineCenterOfAll() const
 {
-  molecule::const_iterator iter = begin();  // start at first in list
+  const_iterator iter = begin();  // start at first in list
   Vector *a = new Vector();
   double Num = 0;
@@ -174 +174 @@
 Vector * molecule::DetermineCenterOfGravity() const
 {
-  molecule::const_iterator iter = begin();  // start at first in list
+  const_iterator iter = begin();  // start at first in list
   Vector *a = new Vector();
   Vector tmp;
@@ -202 +202 @@
   DeterminePeriodicCenter(NewCenter);
   // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    *iter -= NewCenter;
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    **iter -= NewCenter;
   }
 };
@@ -215 +215 @@
 {
   // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    *iter -= *newcenter;
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    **iter -= *newcenter;
   }
 };
@@ -233 +233 @@
 
   // sum up inertia tensor
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (const_iterator iter = begin(); iter != end(); ++iter) {
     Vector x = (*iter)->getPosition();
     x -= *CenterOfGravity;
@@ -286 +286 @@
 
   // and rotate
-  for (molecule::iterator iter = begin(); iter != end(); ++iter) {
+  for (iterator iter = begin(); iter != end(); ++iter) {
     *(*iter) -= *CenterOfGravity;
     (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), alpha));
@@ -306 +306 @@
 void molecule::Scale(const double ** const factor)
 {
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (iterator iter = begin(); iter != end(); ++iter) {
     for (size_t j=0;j<(*iter)->getTrajectorySize();j++) {
       Vector temp = (*iter)->getPositionAtStep(j);
@@ -320 +320 @@
 void molecule::Translate(const Vector *trans)
 {
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (iterator iter = begin(); iter != end(); ++iter) {
     for (size_t j=0;j<(*iter)->getTrajectorySize();j++) {
       (*iter)->setPositionAtStep(j, (*iter)->getPositionAtStep(j) + (*trans));
@@ -336 +336 @@
 
   // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    *iter += *trans;
-  }
-  atoms.transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    **iter += *trans;
+  }
+  getAtomSet().transformNodes(boost::bind(&Box::WrapPeriodically,domain,_1));
 
 };
@@ -351 +351 @@
   OBSERVE;
   Plane p(*n,0);
-  atoms.transformNodes(boost::bind(&Plane::mirrorVector,p,_1));
+  getAtomSet().transformNodes(boost::bind(&Plane::mirrorVector,p,_1));
 };
 
@@ -371 +371 @@
     Center.Zero();
     flag = true;
-    for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    for (const_iterator iter = begin(); iter != end(); ++iter) {
       if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) {
         Testvector = inversematrix * (*iter)->getPosition();
@@ -435 +435 @@
   alpha = atan(-n->at(0)/n->at(2));
   LOG(1, "INFO: Z-X-angle: " << alpha << " ... ");
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (iterator iter = begin(); iter != end(); ++iter) {
     tmp = (*iter)->at(0);
     (*iter)->set(0,  cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));
@@ -455 +455 @@
   alpha = atan(-n->at(1)/n->at(2));
   LOG(1, "INFO: Z-Y-angle: " << alpha << " ... ");
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+  for (iterator iter = begin(); iter != end(); ++iter) {
     tmp = (*iter)->at(1);
     (*iter)->set(1,  cos(alpha) * tmp + sin(alpha) * (*iter)->at(2));

src/molecule_graph.cpp

@@ -52 +52 @@
 bool molecule::FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList)
 {
-  atom *OtherWalker = NULL;
-  atom *Father = NULL;
-  bool status = true;
-  int AtomNo;
+  bool status = true;
 
   LOG(1, "Begin of FillBondStructureFromReference.");
@@ -71 +68 @@
 
 
-    for(molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-      Father = (*iter)->GetTrueFather();
-      AtomNo = Father->getNr(); // global id of the current walker
+    for(molecule::iterator iter = begin(); iter != end(); ++iter) {
+      const atom * const Father = (*iter)->GetTrueFather();
+      const int AtomNo = Father->getNr(); // global id of the current walker
       const BondList& ListOfBonds = Father->getListOfBonds();
       for (BondList::const_iterator Runner = ListOfBonds.begin();
           Runner != ListOfBonds.end();
           ++Runner) {
-        OtherWalker = ListOfLocalAtoms[(*Runner)->GetOtherAtom((*iter)->GetTrueFather())->getNr()]; // local copy of current bond partner of walker
+        atom * const OtherAtom = (*Runner)->GetOtherAtom((*iter)->GetTrueFather());
+        atom * const OtherWalker = ListOfLocalAtoms[OtherAtom->getNr()]; // local copy of current bond partner of walker
         if (OtherWalker != NULL) {
           if (OtherWalker->getNr() > (*iter)->getNr())
             AddBond((*iter), OtherWalker, (*Runner)->BondDegree);
         } else {
-          LOG(1, "OtherWalker = ListOfLocalAtoms[" << (*Runner)->GetOtherAtom((*iter)->GetTrueFather())->getNr() << "] is NULL!");
+          LOG(1, "OtherWalker = ListOfLocalAtoms[" << OtherAtom->getNr() << "] is NULL!");
           status = false;
         }
@@ -154 +152 @@
   if (AdjacencyFile.good()) {
     AdjacencyFile << "m\tn" << endl;
-    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputAdjacency),&AdjacencyFile));
+    for_each(begin(),end(),bind2nd(mem_fun(&atom::OutputAdjacency),&AdjacencyFile));
     AdjacencyFile.close();
     LOG(1, "\t... done.");
@@ -186 +184 @@
   if (BondFile.good()) {
     BondFile << "m\tn" << endl;
-    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputBonds),&BondFile));
+    for_each(begin(),end(),bind2nd(mem_fun(&atom::OutputBonds),&BondFile));
     BondFile.close();
     LOG(1, "\t... done.");

src/moleculelist.cpp

@@ -571 +571 @@
       // output file
       std::vector<atom *> atoms;
-      for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
+      // TODO: Convert iterator to const_iterator when FormatParserStorage::save() has vector<const atom *>
+      // We need iterator here because FormatParserStorage::save() need vector<atom *> not const refs.
+      for (molecule::iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
         atoms.push_back(*iter);
       }