Changeset 129204 for src/Bond

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/Bond

Files:

• GraphEdge.cpp (added)
• GraphEdge.hpp (added)
• bond.cpp (moved) (moved from src/bond.cpp ) (7 diffs)
• bond.hpp (moved) (moved from src/bond.hpp ) (5 diffs)

src/Bond/bond.cpp

@@ -6 +6 @@
  */
 
-/** \file bond.cpp
+/** \file Bond.cpp
  * 
  * Function implementations for the classes BondLeaf, BondTree and bond.
@@ -22 +22 @@
 #include "CodePatterns/Verbose.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "element.hpp"
 
@@ -35 +35 @@
   HydrogenBond(0),
   BondDegree(0),
-  nr(-1),
-  Cyclic(false),
-  Type(Undetermined),
-  Used(white)
+  nr(-1)
 {};
 
@@ -52 +49 @@
   HydrogenBond(0),
   BondDegree(degree),
-  nr(number),
-  Cyclic(false),
-  Type(Undetermined),
-  Used(white)
+  nr(number)
 {
   if ((left != NULL) && (right != NULL)) {
@@ -97 +91 @@
 
 
-/** Returns whether vertex was used in DFS.
- * \return bond::Used
- */
-enum bond::Shading bond::IsUsed()
-{
-  return Used;
-};
-
 /** Checks if an atom exists in a bond.
  * \param *ptr pointer to atom
@@ -123 +109 @@
 };
 
-/** Masks vertex as used in DFS.
- * \return bond::Used, false if bond was already marked used
- */
-bool bond::MarkUsed(const enum Shading color) {
-  if (Used == black) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Bond " << this << " was already marked black!." << endl);
-    return false;
-  } else {
-    Used = color;
-    return true;
-  }
-};
-
-/** Resets used flag in DFS.
- * \return bond::Used
- */
-void bond::ResetUsed() {
-  Used = white;
-};
-
 /** Calculates the bond length.
  * \return |a - b| with a = bond::leftatom and b = bond::rightatom.
@@ -158 +124 @@
   return (leftatom->DistanceSquared(*rightatom));
 };
-
-/** Returns Shading as a char string.
- * \param color the Shading
- * \return string of the flag
- */
-string bond::getColorName(enum Shading color)
-{
-  switch (color) {
-    case white:
-      return "white";
-      break;
-    case lightgray:
-      return "lightgray";
-      break;
-    case darkgray:
-      return "darkgray";
-      break;
-    case black:
-      return "black";
-      break;
-    default:
-      return "uncolored";
-      break;
-  };
-}

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()
 };