Changeset 88c8ec for src/Graph/DepthFirstSearchAnalysis.hpp

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/Graph/DepthFirstSearchAnalysis.hpp (modified) (8 diffs)

src/Graph/DepthFirstSearchAnalysis.hpp

@@ -16 +16 @@
 #include <deque>
 
+#include "Bond/bond.hpp"
 #include "ConnectedSubgraph.hpp"
 
 class atom;
-class bond;
 class ListOfLocalAtoms_t;
 class MoleculeLeafClass;
@@ -39 +39 @@
    * articulations points, ...
    * We use the algorithm from [Even, Graph Algorithms, p.62].
-   * \param *&BackEdgeStack NULL pointer to std::deque<bond *> with all the found back edges, allocated and filled on return
+   * \param *&BackEdgeStack NULL pointer to std::deque<bond::ptr > with all the found back edges, allocated and filled on return
    * \return list of each disconnected subgraph as an individual molecule class structure
    */
@@ -71 +71 @@
    * \return true - everything ok, false - ReferenceStack was empty
    */
-  bool PickLocalBackEdges(const ListOfLocalAtoms_t &ListOfLocalAtoms, std::deque<bond *> *&LocalStack) const;
+  bool PickLocalBackEdges(const ListOfLocalAtoms_t &ListOfLocalAtoms, std::deque<bond::ptr > *&LocalStack) const;
 
   /** Getter for BackEdgeStack.
@@ -77 +77 @@
    * @return const reference to BackEdgeStack
    */
-  const std::deque<bond *>& getBackEdgeStack() const;
+  const std::deque<bond::ptr >& getBackEdgeStack() const;
 
 private:
@@ -89 +89 @@
    * \return bond class or NULL
    */
-  bond * FindNextUnused(atom *vertex) const;
+  bond::ptr FindNextUnused(atom *vertex) const;
 
   /** Resets bond::Used flag of all bonds in this molecule.
@@ -116 +116 @@
    * \param *&Binder current edge
    */
-  void ProbeAlongUnusedBond(atom *&Walker, bond *&Binder);
+  void ProbeAlongUnusedBond(atom *&Walker, bond::ptr &Binder);
 
   /** Checks whether we have a new component.
@@ -134 +134 @@
    * \param &LeafWalker contains reference to destination subgraph
    */
-  void CleanRootStackDownTillWalker(atom *&Walker, bond *&Binder, ConnectedSubgraph &LeafWalker);
+  void CleanRootStackDownTillWalker(atom *&Walker, bond::ptr &Binder, ConnectedSubgraph &LeafWalker);
 
   /** Output graph information per atom.
@@ -145 +145 @@
 
   std::deque<atom *> AtomStack;
-  std::deque<bond *> BackEdgeStack;
+  std::deque<bond::ptr > BackEdgeStack;
   int CurrentGraphNr;
   int ComponentNumber;