Changeset 129204 for src/Bond/bond.hpp

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.

File:

• src/Bond/bond.hpp (moved) (moved from src/bond.hpp ) (5 diffs)

src/Bond/bond.hpp

@@ -1 +1 @@
 /*
- * bond.hpp
+ * Bond.hpp
  *
  *  Created on: Aug 3, 2009
@@ -18 +18 @@
 #endif
 
+#include "Bond/GraphEdge.hpp"
+
 /****************************************** forward declarations *****************************/
 
@@ -28 +30 @@
  * Class incorporates bonds between atoms in a molecule.
  * Note that we regard bond always as something in a molecule,
- * as it is the glue making up the connected subgrapgh and
+ * as it is the glue making up the connected subgraph and
  * hence the molecule. Thus, bonds belong globally to the molecule
- * (and are free'd there) and only locally to the atom classs.
+ * (and are free'd there) and only locally to the atom class.
  */
-class bond {
+class bond : public GraphEdge
+{
   public:
-  enum EdgeType { Undetermined, TreeEdge, BackEdge }; //!< edge type in a graph after Depth-First-Search analysis.
-
-  enum Shading { white, lightgray, darkgray, black };  //!< color in Breadth-First-Search analysis
-
   atom *leftatom;    //!< first bond partner
   atom *rightatom;  //!< second bond partner
@@ -43 +42 @@
   int BondDegree;    //!< single, double, triple, ... bond
   int nr;           //!< unique number in a molecule, updated by BondGraph::CreateAdjacencyForList()
-  bool Cyclic;      //!< flag whether bond is part of a cycle or not, given in DepthFirstSearchAnalysis()
-  enum EdgeType Type;//!< whether this is a tree or back edge
 
   atom * GetOtherAtom(const ParticleInfo * const Atom) const;
 
-  bool MarkUsed(const enum Shading color);
-  enum Shading IsUsed();
-  void ResetUsed();
   bool Contains(const ParticleInfo * const ptr);
   bool Contains(const int nr);
@@ -60 +54 @@
   ~bond();
 
-  static std::string getColorName(enum Shading color);
-
-  private:
-    enum Shading Used;        //!< marker in depth-first search, DepthFirstSearchAnalysis()
 };