Changeset 59fff1 for src/molecule.cpp

Timestamp:

Dec 28, 2011, 3:25:49 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:

afa9d8

Parents:

30c753

git-author:

Frederik Heber <heber@…> (12/23/11 10:09:37)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:25:49)

Message:

Replaced the molecule::const_iterator by a true const version of the transform_iterator.

• lots of places used const_iterator where it made no sense, atom some others one could have sensibly done so but details prevented it, e.g.
  • FormatParserStorage::save() requires vector<atom*> not const atom *,
  • Boundaries (and most of Tesselation for that) requires atom *, not const atom *.
• Added new function molecule::isInMolecule() to check whether atomic id is in molecule::atomIds.
• Added const version of atom::GetTrueFather().

File:

• src/molecule.cpp (modified) (11 diffs)

src/molecule.cpp

@@ -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;
+  const_iterator iter = loc;
   ++iter;
-  atom* atom = *loc;
-  atomIds.erase( atom->getId() );
-  formula-=atom->getType();
-  atom->removeFromMolecule();
+  atom * const _atom = const_cast<atom *>(*loc);
+  atomIds.erase( _atom->getId() );
+  formula-=_atom->getType();
+  _atom->removeFromMolecule();
   return iter;
 }
@@ -193 +193 @@
 {
   OBSERVE;
-  molecule::const_iterator iter = find(key);
+  const_iterator iter = find(key);
   if (iter != end()){
     ++iter;
@@ -233 +233 @@
 //      iter != MyIter(atomIds.end(), FromIdToAtom());
 //      ++iter)
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter)
+  for (molecule::iterator iter = begin(); iter != end(); ++iter)
     vector_of_atoms.push_back(*iter);
   return vector_of_atoms;
@@ -634 +634 @@
   // copy all atoms
   std::map< const atom *, atom *> FatherFinder;
-  for (const_iterator iter = begin(); iter != end(); ++iter) {
-    atom *const copy_atom = copy->AddCopyAtom(*iter);
+  for (iterator iter = begin(); iter != end(); ++iter) {
+    atom * const copy_atom = copy->AddCopyAtom(*iter);
     FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
   }
@@ -649 +649 @@
         // get the pendant atoms of current bond in the copy molecule
         ASSERT(FatherFinder.count(Binder->leftatom),
-            "molecule::CopyMolecule() - No copy of original left atom for bond copy found");
+            "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 for bond copy found");
+            "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];
@@ -674 +676 @@
 {
   // remove each atom from world
-  for(const_iterator AtomRunner = begin(); !empty(); AtomRunner = begin())
+  for(iterator AtomRunner = begin(); !empty(); AtomRunner = begin())
     World::getInstance().destroyAtom(*AtomRunner);
 };
@@ -690 +692 @@
   // copy all atoms
   std::map< const atom *, atom *> FatherFinder;
-  for (const_iterator iter = begin(); iter != end(); ++iter) {
+  for (iterator iter = begin(); iter != end(); ++iter) {
     if((*iter)->IsInShape(region)){
-      atom *const copy_atom = copy->AddCopyAtom(*iter);
+      atom * const copy_atom = copy->AddCopyAtom(*iter);
       FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
     }
@@ -739 +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++;
 
@@ -850 +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.
@@ -1002 +1031 @@
   int i = 0;
   NoNonHydrogen = 0;
-  for (molecule::const_iterator iter = begin(); iter != 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