Changeset 129204 for src/Graph

Timestamp:

Mar 2, 2011, 9:53:08 PM (14 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:

111387

Parents:

766ba5

git-author:

Frederik Heber <heber@…> (02/25/11 19:58:54)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:08)

Message:

Moved bond.* to Bond/, new class GraphEdge which contains graph parts of bond.

• enums Shading and EdgeType are now part of GraphEdge, hence bigger change in the code where these are used.

Location:

src/Graph

Files:

• BondGraph.cpp (modified) (1 diff)
• BondGraph.hpp (modified) (1 diff)
• BreadthFirstSearchAdd.cpp (modified) (8 diffs)
• BreadthFirstSearchAdd.hpp (modified) (2 diffs)

src/Graph/BondGraph.cpp

@@ -23 +23 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Box.hpp"

src/Graph/BondGraph.hpp

@@ -21 +21 @@
 
 #include "AtomSet.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"

src/Graph/BreadthFirstSearchAdd.cpp

@@ -23 +23 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Info.hpp"
@@ -57 +57 @@
   ShortestPathList[atom_id] = -1;
   if (AddedAtomList.find(atom_id) != AddedAtomList.end()) // mark already present atoms (i.e. Root and maybe others) as visited
-    ColorList[atom_id] = bond::lightgray;
+    ColorList[atom_id] = GraphEdge::lightgray;
   else
-    ColorList[atom_id] = bond::white;
+    ColorList[atom_id] = GraphEdge::white;
 }
 
@@ -65 +65 @@
 void BreadthFirstSearchAdd::UnvisitedNode(molecule *Mol, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond)
 {
-  if (Binder != Bond) // let other atom bond::white if it's via Root bond. In case it's cyclic it has to be reached again (yet Root is from OtherAtom already bond::black, thus no problem)
-    ColorList[OtherAtom->getNr()] = bond::lightgray;
+  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)
+    ColorList[OtherAtom->getNr()] = GraphEdge::lightgray;
   PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
   ShortestPathList[OtherAtom->getNr()] = ShortestPathList[Walker->getNr()] + 1;
-  DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " " << Binder->getColorName(ColorList[OtherAtom->getNr()]) << ", its predecessor is " << Walker->getName() << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl);
+  DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " " << GraphEdge::getColorName(ColorList[OtherAtom->getNr()]) << ", its predecessor is " << Walker->getName() << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl);
   if ((((ShortestPathList[OtherAtom->getNr()] < BondOrder) && (Binder != Bond)))) { // Check for maximum distance
     DoLog(3) && (Log() << Verbose(3));
@@ -77 +77 @@
       AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
       DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder->nr]) << ", ");
-    } else { // this code should actually never come into play (all bond::white atoms are not yet present in BondMolecule, that's why they are bond::white in the first place)
+    } else { // this code should actually never come into play (all GraphEdge::white atoms are not yet present in BondMolecule, that's why they are GraphEdge::white in the first place)
       DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->getName());
       if (AddedBondList[Binder->nr] == NULL) {
@@ -89 +89 @@
   } else { // out of bond order, then replace
     if ((AddedAtomList[OtherAtom->getNr()] == NULL) && (Binder->Cyclic))
-      ColorList[OtherAtom->getNr()] = bond::white; // unmark if it has not been queued/added, to make it available via its other bonds (cyclic)
+      ColorList[OtherAtom->getNr()] = GraphEdge::white; // unmark if it has not been queued/added, to make it available via its other bonds (cyclic)
     if (Binder == Bond)
       DoLog(3) && (Log() << Verbose(3) << "Not Queueing, is the Root bond");
@@ -139 +139 @@
   Init(_Root, _BondOrder);
 
-  // and go on ... Queue always contains all bond::lightgray vertices
+  // and go on ... Queue always contains all GraphEdge::lightgray vertices
   while (!BFSStack.empty()) {
     // we have to pop the oldest atom from stack. This keeps the atoms on the stack always of the same ShortestPath distance.
@@ -156 +156 @@
         OtherAtom = (*Runner)->GetOtherAtom(Walker);
         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
-        if (ColorList[OtherAtom->getNr()] == bond::white) {
+        if (ColorList[OtherAtom->getNr()] == GraphEdge::white) {
           UnvisitedNode(Mol, Walker, OtherAtom, Binder, Bond);
         } else {
@@ -163 +163 @@
       }
     }
-    ColorList[Walker->getNr()] = bond::black;
-    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " bond::black." << endl);
+    ColorList[Walker->getNr()] = GraphEdge::black;
+    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " GraphEdge::black." << endl);
   }
 }

src/Graph/BreadthFirstSearchAdd.hpp

@@ -20 +20 @@
 #include "types.hpp"
 
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 
 class atom;
@@ -60 +60 @@
   std::map<atomId_t, atom *> PredecessorList;
   std::map<atomId_t, int > ShortestPathList;
-  std::map<atomId_t, enum bond::Shading> ColorList;
+  std::map<atomId_t, enum GraphEdge::Shading> ColorList;
   std::deque<atom *> BFSStack;
   int BondOrder;