Changeset f01769 for src/molecule.cpp

Timestamp:

Jul 24, 2015, 4:44:34 PM (10 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:

a58c16

Parents:

1259df

git-author:

Frederik Heber <heber@…> (06/01/15 16:57:36)

git-committer:

Frederik Heber <heber@…> (07/24/15 16:44:34)

Message:

Replaced World::getAtom() wherever possible by const version.

• some AtomSet member functions now have const atom ptr instead of atom ptr.
• molecule can return const and non-const AtomSet.
• added FromIdToConstAtom to allow iterate through atoms in molecule (which are stored by id, not by ptr) in const fashion.
• in molecule::isInMolecule() is now const, ::CopyMolecule..() is non-const (because copying involves father atom who is stored non-const).

File:

• src/molecule.cpp (modified) (9 diffs)

src/molecule.cpp

@@ -242 +242 @@
     NOTIFY(AtomRemoved);
   }
-  const_iterator iter = find(key);
-  if (iter != end()){
+  const_iterator iter = const_cast<const molecule &>(*this).find(key);
+  if (iter != const_cast<const molecule &>(*this).end()){
     ++iter;
     atomIds.erase( key->getId() );
@@ -285 +285 @@
 }
 
-World::AtomComposite molecule::getAtomSet() const
+World::AtomComposite molecule::getAtomSet()
 {
   World::AtomComposite vector_of_atoms;
   for (molecule::iterator iter = begin(); iter != end(); ++iter)
+    vector_of_atoms.push_back(*iter);
+  return vector_of_atoms;
+}
+
+World::ConstAtomComposite molecule::getAtomSet() const
+{
+  World::ConstAtomComposite vector_of_atoms;
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter)
     vector_of_atoms.push_back(*iter);
   return vector_of_atoms;
@@ -609 +617 @@
  * \return copy of molecule
  */
-molecule *molecule::CopyMolecule(const Vector &offset) const
+molecule *molecule::CopyMolecule(const Vector &offset)
 {
   molecule *copy = World::getInstance().createMolecule();
@@ -622 +630 @@
 
   // copy all bonds
-  for(const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
+  for(const_iterator AtomRunner = const_cast<const molecule &>(*this).begin();
+      AtomRunner != const_cast<const molecule &>(*this).end();
+      ++AtomRunner) {
     const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
     for(BondList::const_iterator BondRunner = ListOfBonds.begin();
@@ -676 +686 @@
  * @param three vectors forming the matrix that defines the shape of the parallelpiped
  */
-molecule* molecule::CopyMoleculeFromSubRegion(const Shape &region) const {
+molecule* molecule::CopyMoleculeFromSubRegion(const Shape &region) {
   molecule *copy = World::getInstance().createMolecule();
 
@@ -689 +699 @@
 
   // copy all bonds
-  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
+  for(molecule::const_iterator AtomRunner = const_cast<const molecule &>(*this).begin();
+      AtomRunner != const_cast<const molecule &>(*this).end();
+      ++AtomRunner) {
     const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
     for(BondList::const_iterator BondRunner = ListOfBonds.begin();
@@ -821 +833 @@
  * @return true - is member, false - is not
  */
-bool molecule::isInMolecule(const atom * const _atom)
+bool molecule::isInMolecule(const atom * const _atom) const
 {
   ASSERT(_atom->getMolecule() == this,
@@ -934 +946 @@
  * \todo make this with a good sort O(n), not O(n^2)
  */
-int * molecule::GetFatherSonAtomicMap(molecule *OtherMolecule)
+int * molecule::GetFatherSonAtomicMap(const molecule * const OtherMolecule)
 {
   LOG(3, "Begin of GetFatherAtomicMap.");
@@ -947 +959 @@
     std::stringstream output;
     output << "Map is ";
-    for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    for (molecule::const_iterator iter = const_cast<const molecule &>(*this).begin();
+        iter != const_cast<const molecule &>(*this).end();
+        ++iter) {
       if ((*iter)->getFather() == NULL) {
         AtomicMap[(*iter)->getNr()] = -2;