Changeset 88c8ec for src/molecule.cpp

Timestamp:

Jan 17, 2013, 10:59:15 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, 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:

c8302f3

Parents:

d6b6ce

git-author:

Frederik Heber <heber@…> (10/29/12 00:28:46)

git-committer:

Frederik Heber <heber@…> (01/17/13 22:59:15)

Message:

REFACTOR: Replaced all "bond *" appearances by bond::ptr.

• this is preparatory for making bond::ptr a boost::shared_ptr of bond.
• NOTE: We had to remove a const prefix at four or five places and forward declarations had to be replaced by the true inclusion of bond.hpp at tne or so files. Apart from that, the replacement has been very smooth.

File:

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

src/molecule.cpp

@@ -326 +326 @@
  * \todo double and triple bonds splitting (always use the tetraeder angle!)
  */
-bool molecule::AddHydrogenReplacementAtom(bond *TopBond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem)
+bool molecule::AddHydrogenReplacementAtom(bond::ptr TopBond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem)
 {
 //  Info info(__func__);
@@ -333 +333 @@
   double bondangle;  // bond angle of the bond to be replaced/cut
   double BondRescale;   // rescale value for the hydrogen bond length
-  bond *FirstBond = NULL, *SecondBond = NULL; // Other bonds in double bond case to determine "other" plane
+  bond::ptr FirstBond = NULL;
+  bond::ptr SecondBond = NULL; // Other bonds in double bond case to determine "other" plane
   atom *FirstOtherAtom = NULL, *SecondOtherAtom = NULL, *ThirdOtherAtom = NULL; // pointer to hydrogen atoms to be added
   double b,l,d,f,g, alpha, factors[NDIM];    // hold temporary values in triple bond case for coordination determination
@@ -339 +340 @@
   Vector InBondvector;    // vector in direction of *Bond
   const RealSpaceMatrix &matrix =  World::getInstance().getDomain().getM();
-  bond *Binder = NULL;
+  bond::ptr Binder = NULL;
 
   // create vector in direction of bond
@@ -596 +597 @@
         ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner) {
-        bond *Binder = (*BondRunner);
+        bond::ptr Binder = (*BondRunner);
         // get the pendant atoms of current bond in the copy molecule
         ASSERT(FatherFinder.count(Binder->leftatom),
@@ -607 +608 @@
         atom * const RightAtom = FatherFinder[Binder->rightatom];
 
-        bond * const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
+        bond::ptr const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
         NewBond->Cyclic = Binder->Cyclic;
         if (Binder->Cyclic)
@@ -656 +657 @@
         ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner) {
-        bond *Binder = (*BondRunner);
+        bond::ptr Binder = (*BondRunner);
         if ((FatherFinder.count(Binder->leftatom))
             && (FatherFinder.count(Binder->rightatom))) {
@@ -663 +664 @@
           atom * const RightAtom = FatherFinder[Binder->rightatom];
 
-          bond * const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
+          bond::ptr const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
           NewBond->Cyclic = Binder->Cyclic;
           if (Binder->Cyclic)
@@ -685 +686 @@
  * \return pointer to bond or NULL on failure
  */
-bond * molecule::AddBond(atom *atom1, atom *atom2, int degree)
-{
-  bond *Binder = NULL;
+bond::ptr molecule::AddBond(atom *atom1, atom *atom2, int degree)
+{
+  bond::ptr Binder = NULL;
 
   // some checks to make sure we are able to create the bond
@@ -720 +721 @@
  * \return true - bound found and removed, false - bond not found/removed
  */
-bool molecule::RemoveBond(bond *pointer)
+bool molecule::RemoveBond(bond::ptr pointer)
 {
   //ELOG(1, "molecule::RemoveBond: Function not implemented yet.");