Changeset e08c46 for src/molecule.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/molecule.cpp (modified) (8 diffs)

src/molecule.cpp

@@ -36 +36 @@
  */
 molecule::molecule(const periodentafel * const teil) : elemente(teil),
-  first(new bond(0, 0, 1, -1)), last(new bond(0, 0, 1, -1)), MDSteps(0),
+  MDSteps(0),
   BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.), 
   ActiveFlag(false), IndexNr(-1),
@@ -42 +42 @@
   AtomCount(this,boost::bind(&molecule::doCountAtoms,this)), last_atom(0),  InternalPointer(begin())
 {
-  // init bond chain list
-  link(first,last);
 
   // other stuff
@@ -61 +59 @@
 {
   CleanupMolecule();
-  delete(first);
-  delete(last);
 };
 
@@ -607 +603 @@
 
   // copy all bonds
-  bond *Binder = first;
+  bond *Binder = NULL;
   bond *NewBond = NULL;
-  while(Binder->next != last) {
-    Binder = Binder->next;
-
-    // get the pendant atoms of current bond in the copy molecule
-    copy->ActOnAllAtoms( &atom::EqualsFather, (const atom *)Binder->leftatom, (const atom **)&LeftAtom );
-    copy->ActOnAllAtoms( &atom::EqualsFather, (const atom *)Binder->rightatom, (const atom **)&RightAtom );
-
-    NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
-    NewBond->Cyclic = Binder->Cyclic;
-    if (Binder->Cyclic)
-      copy->NoCyclicBonds++;
-    NewBond->Type = Binder->Type;
-  }
+  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+      if ((*BondRunner)->leftatom == *AtomRunner) {
+        Binder = (*BondRunner);
+
+        // get the pendant atoms of current bond in the copy molecule
+        copy->ActOnAllAtoms( &atom::EqualsFather, (const atom *)Binder->leftatom, (const atom **)&LeftAtom );
+        copy->ActOnAllAtoms( &atom::EqualsFather, (const atom *)Binder->rightatom, (const atom **)&RightAtom );
+
+        NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
+        NewBond->Cyclic = Binder->Cyclic;
+        if (Binder->Cyclic)
+          copy->NoCyclicBonds++;
+        NewBond->Type = Binder->Type;
+      }
   // correct fathers
   ActOnAllAtoms( &atom::CorrectFather );
@@ -627 +625 @@
   // copy values
   copy->CountElements();
-  if (first->next != last) {  // if adjaceny list is present
+  if (hasBondStructure()) {  // if adjaceny list is present
     copy->BondDistance = BondDistance;
   }
@@ -672 +670 @@
   if ((atom1->type != NULL) && (atom1->type->Z != 1) && (atom2->type != NULL) && (atom2->type->Z != 1))
     NoNonBonds++;
-  add(Binder, last);
 
   return Binder;
@@ -685 +682 @@
 {
   //DoeLog(1) && (eLog()<< Verbose(1) << "molecule::RemoveBond: Function not implemented yet." << endl);
-  pointer->leftatom->RegisterBond(pointer);
-  pointer->rightatom->RegisterBond(pointer);
-  removewithoutcheck(pointer);
+  delete(pointer);
   return true;
 };
@@ -785 +780 @@
   for (molecule::iterator iter = begin(); !empty(); iter = begin())
       erase(iter);
-  return (cleanup(first,last));
 };