Changeset e08c46 for src/moleculelist.cpp

Timestamp:

May 31, 2010, 6:41:12 PM (15 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:

1b9321

Parents:

1024cb

Message:

Removed molecule::first, molecule::last.

• molecule does not have a chained list of bonds.
• we have to go through atoms and its bonds, by checking (*BondRunner)->leftatom against (*AtomRunner) we exclude the other half.
• first,last were present in only a few structures.
• new functions:
  • molecule::hasBondStructure() - replaces first->next != last construct
  • molecule::CountBonds() - replaces first->next->next == last (i.e. one bond present) and alikes.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/moleculelist.cpp (modified) (5 diffs)

src/moleculelist.cpp

@@ -345 +345 @@
 
   // go through all bonds and add as well
-  bond *Binder = srcmol->first;
-  while(Binder->next != srcmol->last) {
-    Binder = Binder->next;
-    DoLog(3) && (Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl);
-    mol->AddBond(CopyAtoms[Binder->leftatom->nr], CopyAtoms[Binder->rightatom->nr], Binder->BondDegree);
-  }
+  for(molecule::iterator AtomRunner = srcmol->begin(); AtomRunner != srcmol->end(); ++AtomRunner)
+    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+      if ((*BondRunner)->leftatom == *AtomRunner) {
+        DoLog(3) && (Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[(*BondRunner)->leftatom->nr] << " and " << *CopyAtoms[(*BondRunner)->rightatom->nr]<< "." << endl);
+        mol->AddBond(CopyAtoms[(*BondRunner)->leftatom->nr], CopyAtoms[(*BondRunner)->rightatom->nr], (*BondRunner)->BondDegree);
+      }
   delete(LCList);
   return true;
@@ -744 +744 @@
   molecule *mol = World::getInstance().createMolecule();
   bond *Binder = NULL;
-  bond *Stepper = NULL;
   // 0. gather all atoms into single molecule
   for (MoleculeList::iterator MolRunner = ListOfMolecules.begin(); !ListOfMolecules.empty(); MolRunner = ListOfMolecules.begin()) {
@@ -755 +754 @@
     }
     // remove all bonds
-    Stepper = (*MolRunner)->first->next;
-    while (Stepper != (*MolRunner)->last) {
-      Binder = Stepper;
-      Stepper = Stepper->next;
-      delete(Binder);
-    }
+    for(molecule::iterator AtomRunner = (*MolRunner)->begin(); AtomRunner != (*MolRunner)->end(); ++AtomRunner)
+      for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+        delete(*BondRunner);
     // remove the molecule
     World::getInstance().destroyMolecule(*MolRunner);
@@ -835 +831 @@
   }
   // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
-  Binder = mol->first;
-  while (mol->first->next != mol->last) {
-    Binder = mol->first->next;
-    const atom * const Walker = Binder->leftatom;
-    unlink(Binder);
-    link(Binder,molecules[MolMap[Walker->nr]-1]->last);   // counting starts at 1
-  }
+  // TODO: check whether this is really not needed anymore
   // 4e. free Leafs
   MolecularWalker = Subgraphs;
@@ -1052 +1042 @@
     DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl);
     // remove every bond from the list
-    bond *Binder = NULL;
-    while (Leaf->last->previous != Leaf->first) {
-      Binder = Leaf->last->previous;
-      Binder->leftatom->UnregisterBond(Binder);
-      Binder->rightatom->UnregisterBond(Binder);
-      removewithoutcheck(Binder);
-    }
+    for(molecule::iterator AtomRunner = Leaf->begin(); AtomRunner != Leaf->end(); ++AtomRunner)
+      for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+        if ((*BondRunner)->leftatom == *AtomRunner)
+          delete((*BondRunner));
 
     for(molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ++iter) {