Changeset fd4905 for src/molecule.cpp

Timestamp:

Aug 28, 2010, 1:45:13 AM (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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

6c438f

Parents:

8fd934 (diff), 653542 (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 'stable' into StructureRefactoring

File:

• src/molecule.cpp (modified) (6 diffs)

src/molecule.cpp

@@ -83 +83 @@
 
 // getter and setter
-const std::string molecule::getName(){
+const std::string molecule::getName() const{
   return std::string(name);
 }
@@ -110 +110 @@
 
 
-moleculeId_t molecule::getId(){
+moleculeId_t molecule::getId() const {
   return id;
 }
@@ -118 +118 @@
 }
 
-const Formula &molecule::getFormula(){
+const Formula &molecule::getFormula() const {
   return formula;
 }
 
-unsigned int molecule::getElementCount(){
+unsigned int molecule::getElementCount() const{
   return formula.getElementCount();
 }
@@ -264 +264 @@
     if ((pointer->getType() != NULL) && (pointer->getType()->getAtomicNumber() != 1))
       NoNonHydrogen++;
+    walker->setMolecule(this);
     retval=walker;
   }
@@ -648 +649 @@
   // copy all bonds
   for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
-    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner) {
         bond *Binder = (*BondRunner);
-
         // get the pendant atoms of current bond in the copy molecule
-        atomSet::iterator leftiter=find_if(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::isFather),Binder->leftatom));
-        atomSet::iterator rightiter=find_if(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::isFather),Binder->rightatom));
-        ASSERT(leftiter!=atoms.end(),"No original left atom for bondcopy found");
-        ASSERT(leftiter!=atoms.end(),"No original right atom for bondcopy found");
+        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;
@@ -713 +713 @@
   ASSERT(atom2, "Second atom in bond-creation was an invalid pointer");
   ASSERT(FindAtom(atom1->nr),"First atom in bond-creation was not part of molecule");
-  ASSERT(FindAtom(atom2->nr),"Second atom in bond-creation was not parto of molecule");
+  ASSERT(FindAtom(atom2->nr),"Second atom in bond-creation was not part of molecule");
 
   Binder = new bond(atom1, atom2, degree, BondCount++);