Changeset 88c8ec for src/Graph

Timestamp:

Jan 17, 2013, 10:59:15 PM (12 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:

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.

Location:

src/Graph

Files:

• BondGraph.hpp (modified) (2 diffs)
• BreadthFirstSearchAdd.cpp (modified) (3 diffs)
• BreadthFirstSearchAdd.hpp (modified) (4 diffs)
• CyclicStructureAnalysis.cpp (modified) (3 diffs)
• CyclicStructureAnalysis.hpp (modified) (4 diffs)
• DepthFirstSearchAnalysis.cpp (modified) (8 diffs)
• DepthFirstSearchAnalysis.hpp (modified) (8 diffs)

src/Graph/BondGraph.hpp

@@ -235 +235 @@
                 LOG(1, "ACCEPT: Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << ".");
                 // directly use iter to avoid const_cast'ing Walker, too
-                //const bond * Binder =
+                //const bond::ptr Binder =
                 const_cast<atom *>(Walker)->addBond(CurrentTime, const_cast<atom *>(OtherWalker));
                 ++BondCount;
@@ -334 +334 @@
 
       LOG(3, "INFO: Creating bond between atoms " << atom1 << " and " << atom2 << ".");
-      //const bond * Binder =
+      //const bond::ptr Binder =
           Walker->addBond(WorldTime::getTime(), OtherWalker);
       bondcounter++;

src/Graph/BreadthFirstSearchAdd.cpp

@@ -81 +81 @@
 
 
-void BreadthFirstSearchAdd::UnvisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond)
+void BreadthFirstSearchAdd::UnvisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond::ptr &Binder, bond::ptr &Bond)
 {
   if (Binder != Bond) // let other atom GraphEdge::white if it's via Root bond. In case it's cyclic it has to be reached again (yet Root is from OtherAtom already GraphEdge::black, thus no problem)
@@ -132 +132 @@
 
 
-void BreadthFirstSearchAdd::VisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond)
+void BreadthFirstSearchAdd::VisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond::ptr &Binder, bond::ptr &Bond)
 {
   LOG(3, "Not Adding, has already been visited.");
@@ -148 +148 @@
 
 
-void BreadthFirstSearchAdd::operator()(molecule *Mol, atom *_Root, bond *Bond, int _BondOrder)
+void BreadthFirstSearchAdd::operator()(molecule *Mol, atom *_Root, bond::ptr Bond, int _BondOrder)
 {
   Info FunctionInfo("BreadthFirstSearchAdd");
   atom *Walker = NULL, *OtherAtom = NULL;
-  bond *Binder = NULL;
+  bond::ptr Binder = NULL;
 
   // add Root if not done yet

src/Graph/BreadthFirstSearchAdd.hpp

@@ -17 +17 @@
 #include <map>
 
+#include "Bond/bond.hpp"
 #include "Bond/GraphEdge.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
@@ -23 +24 @@
 
 class atom;
-class bond;
 class molecule;
 
@@ -48 +48 @@
    * \param IsAngstroem lengths are in angstroem or bohrradii
    */
-  void operator()(molecule *Mol, atom *_Root, bond *Bond, int _BondOrder);
+  void operator()(molecule *Mol, atom *_Root, bond::ptr Bond, int _BondOrder);
 
 private:
-  void UnvisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond);
-  void VisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond);
+  void UnvisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond::ptr &Binder, bond::ptr &Bond);
+  void VisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond::ptr &Binder, bond::ptr &Bond);
 
   /** initialise vertex as white with no predecessor, empty queue, color Root lightgray.
@@ -70 +70 @@
   int ComponentNr;
   std::map<atomId_t, atom *> AddedAtomList;
-  std::map<bond *, bond *> AddedBondList; //!< maps from father bond to son
+  std::map<bond::ptr , bond::ptr > AddedBondList; //!< maps from father bond to son
 
   //!> whether to treat hydrogen special or not

src/Graph/CyclicStructureAnalysis.cpp

@@ -102 +102 @@
  * \param &BFS accounting structure
  */
-void CyclicStructureAnalysis::CyclicBFSFromRootToRoot(bond *&BackEdge)
+void CyclicStructureAnalysis::CyclicBFSFromRootToRoot(bond::ptr &BackEdge)
 {
   atom *Walker = NULL;
@@ -187 +187 @@
  * \param &MinRingSize global minimum distance from one node without encountering oneself, set on return
  */
-void CyclicStructureAnalysis::RetrieveCycleMembers(atom *&OtherAtom, bond *&BackEdge, int &MinRingSize)
+void CyclicStructureAnalysis::RetrieveCycleMembers(atom *&OtherAtom, bond::ptr &BackEdge, int &MinRingSize)
 {
   atom *Walker = NULL;
@@ -327 +327 @@
  * \todo BFS from the not-same-LP to find back to starting point of tributary cycle over more than one bond
  */
-void CyclicStructureAnalysis::operator()(std::deque<bond *> * BackEdgeStack)
+void CyclicStructureAnalysis::operator()(std::deque<bond::ptr > * BackEdgeStack)
 {
   Info FunctionInfo("CyclicStructureAnalysis");
   atom *Walker = NULL;
   atom *OtherAtom = NULL;
-  bond *BackEdge = NULL;
+  bond::ptr BackEdge = NULL;
   int NumCycles = 0;
   int MinRingSize = -1;

src/Graph/CyclicStructureAnalysis.hpp

@@ -17 +17 @@
 #include <map>
 
+#include "Bond/bond.hpp"
 #include "Bond/GraphEdge.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
@@ -23 +24 @@
 
 class atom;
-class bond;
 class molecule;
 
@@ -33 +33 @@
 
   void Reset();
-  void operator()(std::deque<bond *> * BackEdgeStack);
+  void operator()(std::deque<bond::ptr > * BackEdgeStack);
 
   const std::map<atomId_t, int >& getMinimumRingSize() const;
@@ -43 +43 @@
   void InitializeToRoot(atom *&Walker);
   // performing tasks
-  void CyclicBFSFromRootToRoot(bond *&BackEdge);
-  void RetrieveCycleMembers(atom *&OtherAtom, bond *&BackEdge, int &MinRingSize);
+  void CyclicBFSFromRootToRoot(bond::ptr &BackEdge);
+  void RetrieveCycleMembers(atom *&OtherAtom, bond::ptr &BackEdge, int &MinRingSize);
   void BFSToNextCycle(atom *&Root, atom *&Walker);
   void AssignRingSizetoNonCycleMembers(int &MinRingSize, int &NumCycles);

src/Graph/DepthFirstSearchAnalysis.cpp

@@ -77 +77 @@
 
 
-bond * DepthFirstSearchAnalysis::FindNextUnused(atom *vertex) const
+bond::ptr DepthFirstSearchAnalysis::FindNextUnused(atom *vertex) const
 {
   const BondList& ListOfBonds = vertex->getListOfBonds();
@@ -122 +122 @@
 
 
-bool DepthFirstSearchAnalysis::PickLocalBackEdges(const ListOfLocalAtoms_t &ListOfLocalAtoms, std::deque<bond *> *&LocalStack) const
+bool DepthFirstSearchAnalysis::PickLocalBackEdges(const ListOfLocalAtoms_t &ListOfLocalAtoms, std::deque<bond::ptr > *&LocalStack) const
 {
   bool status = true;
@@ -129 +129 @@
     return false;
   }
-  bond *Binder = BackEdgeStack.front();
-  bond *FirstBond = Binder; // mark the first bond, so that we don't loop through the stack indefinitely
+  bond::ptr Binder = BackEdgeStack.front();
+  bond::ptr FirstBond = Binder; // mark the first bond, so that we don't loop through the stack indefinitely
   atom *Walker = NULL, *OtherAtom = NULL;
 
@@ -183 +183 @@
         ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner) {
-        const bond *Binder = *BondRunner;
+        const bond::ptr Binder = *BondRunner;
         if (DoLog(2)) {
           std::stringstream output;
@@ -235 +235 @@
 
 
-void DepthFirstSearchAnalysis::ProbeAlongUnusedBond(atom *&Walker, bond *&Binder)
+void DepthFirstSearchAnalysis::ProbeAlongUnusedBond(atom *&Walker, bond::ptr &Binder)
 {
   atom *OtherAtom = NULL;
@@ -308 +308 @@
 
 
-void DepthFirstSearchAnalysis::CleanRootStackDownTillWalker(atom *&Walker, bond *&Binder, ConnectedSubgraph &Subgraph)
+void DepthFirstSearchAnalysis::CleanRootStackDownTillWalker(atom *&Walker, bond::ptr &Binder, ConnectedSubgraph &Subgraph)
 {
   atom *OtherAtom = NULL;
@@ -343 +343 @@
 
 
-const std::deque<bond *>& DepthFirstSearchAnalysis::getBackEdgeStack() const
+const std::deque<bond::ptr >& DepthFirstSearchAnalysis::getBackEdgeStack() const
 {
   return BackEdgeStack;
@@ -355 +355 @@
   int OldGraphNr = 0;
   atom *Walker = NULL;
-  bond *Binder = NULL;
+  bond::ptr Binder = NULL;
 
   if (World::getInstance().numAtoms() == 0)

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;