Changeset 129204 for src

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

Files:

• Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) (1 diff)
• Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/CopyAction.cpp (modified) (1 diff)
• Bond/GraphEdge.cpp (added)
• Bond/GraphEdge.hpp (added)
• Bond/bond.cpp (moved) (moved from src/bond.cpp ) (7 diffs)
• Bond/bond.hpp (moved) (moved from src/bond.hpp ) (5 diffs)
• Graph/BondGraph.cpp (modified) (1 diff)
• Graph/BondGraph.hpp (modified) (1 diff)
• Graph/BreadthFirstSearchAdd.cpp (modified) (8 diffs)
• Graph/BreadthFirstSearchAdd.hpp (modified) (2 diffs)
• Makefile.am (modified) (5 diffs)
• Parser/PdbParser.cpp (modified) (1 diff)
• Parser/TremoloParser.cpp (modified) (1 diff)
• analysis_bonds.cpp (modified) (1 diff)
• analysis_correlation.cpp (modified) (1 diff)
• atom.cpp (modified) (1 diff)
• atom_bondedparticle.cpp (modified) (1 diff)
• boundary.cpp (modified) (1 diff)
• config.cpp (modified) (2 diffs)
• graph.cpp (modified) (1 diff)
• molecule.cpp (modified) (5 diffs)
• molecule_fragmentation.cpp (modified) (6 diffs)
• molecule_geometry.cpp (modified) (1 diff)
• molecule_graph.cpp (modified) (17 diffs)
• moleculelist.cpp (modified) (2 diffs)
• unittests/AnalysisBondsUnitTest.cpp (modified) (1 diff)
• unittests/BondGraphUnitTest.cpp (modified) (1 diff)
• unittests/CountBondsUnitTest.cpp (modified) (1 diff)
• unittests/ListOfBondsUnitTest.cpp (modified) (1 diff)

src/Actions/FragmentationAction/CreateAdjacencyAction.cpp

@@ -24 +24 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Bond/bond.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Range.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
+#include "Graph/BondGraph.hpp"
 #include "linkedcell.hpp"
 #include "molecule.hpp"

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -24 +24 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Bond/bond.hpp"
 #include "config.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Graph/BondGraph.hpp"
 #include "molecule.hpp"
 #include "World.hpp"

src/Actions/MoleculeAction/CopyAction.cpp

@@ -24 +24 @@
 #include "LinearAlgebra/Vector.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "molecule.hpp"
 #include "World.hpp"

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()
 };
 

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;

src/Makefile.am

@@ -70 +70 @@
   Actions/Process.hpp
 
+BONDSOURCE = \
+        Bond/bond.cpp \
+        Bond/GraphEdge.cpp
+
+BONDHEADER = \
+        Bond/bond.hpp \
+        Bond/GraphEdge.hpp
 
 DESCRIPTORSOURCE = \
@@ -179 +186 @@
   ${ACTIONSSOURCE} \
   ${ATOMSOURCE} \
+  ${BONDSOURCE} \
   ${DESCRIPTORSOURCE} \
   ${DYNAMICSSOURCE} \
@@ -187 +195 @@
   Helpers/defs.cpp \
   Helpers/helpers.cpp \
-  bond.cpp \
   boundary.cpp \
   Box.cpp \
@@ -215 +222 @@
   ${ACTIONSHEADER} \
   ${ATOMHEADER} \
+  ${BONDHEADER} \
   ${DESCRIPTORHEADER} \
   ${DESCRIPTORIMPLHEADER} \
@@ -225 +233 @@
   Helpers/fast_functions.hpp \
   Helpers/helpers.hpp \
-  bond.hpp \
   boundary.hpp \
   Box.hpp \

src/Parser/PdbParser.cpp

@@ -27 +27 @@
 #include "World.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "element.hpp"
 #include "molecule.hpp"

src/Parser/TremoloParser.cpp

@@ -28 +28 @@
 #include "WorldTime.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "element.hpp"
 #include "molecule.hpp"

src/analysis_bonds.cpp

@@ -22 +22 @@
 #include "analysis_bonds.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "element.hpp"
 #include "CodePatterns/Info.hpp"

src/analysis_correlation.cpp

@@ -24 +24 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "BoundaryTriangleSet.hpp"
 #include "Box.hpp"

src/atom.cpp

@@ -20 +20 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "CodePatterns/Log.hpp"
 #include "config.hpp"

src/atom_bondedparticle.cpp

@@ -22 +22 @@
 #include "atom.hpp"
 #include "atom_bondedparticle.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"

src/boundary.cpp

@@ -19 +19 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "boundary.hpp"
 #include "BoundaryLineSet.hpp"

src/config.cpp

@@ -25 +25 @@
 #include <string>
 
-//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Bond/bond.hpp"
+#include "Box.hpp"
+#include "CodePatterns/Info.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
 #include "ConfigFileBuffer.hpp"
 #include "element.hpp"
 #include "Helpers/helpers.hpp"
-#include "CodePatterns/Info.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/toString.hpp"
-#include "CodePatterns/Verbose.hpp"
+#include "Graph/BondGraph.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
 #include "molecule.hpp"
@@ -42 +43 @@
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "Box.hpp"
 
 /************************************* Functions for class config ***************************/

src/graph.cpp

@@ -22 +22 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "config.hpp"
 #include "graph.hpp"

src/molecule.cpp

@@ -27 +27 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Bond/bond.hpp"
 #include "Box.hpp"
 #include "CodePatterns/enumeration.hpp"
@@ -36 +35 @@
 #include "Exceptions/LinearDependenceException.hpp"
 #include "graph.hpp"
+#include "Graph/BondGraph.hpp"
 #include "Helpers/helpers.hpp"
 #include "LinearAlgebra/leastsquaremin.hpp"
@@ -400 +400 @@
       Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
       Binder->Cyclic = false;
-      Binder->Type = bond::TreeEdge;
+      Binder->Type = GraphEdge::TreeEdge;
       break;
     case 2:
@@ -496 +496 @@
       Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
       Binder->Cyclic = false;
-      Binder->Type = bond::TreeEdge;
+      Binder->Type = GraphEdge::TreeEdge;
       Binder = AddBond(BottomOrigin, SecondOtherAtom, 1);
       Binder->Cyclic = false;
-      Binder->Type = bond::TreeEdge;
+      Binder->Type = GraphEdge::TreeEdge;
       break;
     case 3:
@@ -579 +579 @@
       Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
       Binder->Cyclic = false;
-      Binder->Type = bond::TreeEdge;
+      Binder->Type = GraphEdge::TreeEdge;
       Binder = AddBond(BottomOrigin, SecondOtherAtom, 1);
       Binder->Cyclic = false;
-      Binder->Type = bond::TreeEdge;
+      Binder->Type = GraphEdge::TreeEdge;
       Binder = AddBond(BottomOrigin, ThirdOtherAtom, 1);
       Binder->Cyclic = false;
-      Binder->Type = bond::TreeEdge;
+      Binder->Type = GraphEdge::TreeEdge;
       break;
     default:

src/molecule_fragmentation.cpp

@@ -22 +22 @@
 #include <cstring>
 
-#include "World.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Bond/bond.hpp"
+#include "Box.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "CodePatterns/Log.hpp"
 #include "config.hpp"
 #include "element.hpp"
 #include "Helpers/helpers.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
+#include "Graph/BondGraph.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "Box.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -1783 +1782 @@
   atom *OtherWalker = NULL;
   RealSpaceMatrix matrix = World::getInstance().getDomain().getM();
-  enum bond::Shading *ColorList = NULL;
+  enum GraphEdge::Shading *ColorList = NULL;
   double tmp;
   //bool LastBond = true; // only needed to due list construct
@@ -1794 +1793 @@
   DoLog(2) && (Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl);
 
-  ColorList = new enum bond::Shading[getAtomCount()];
+  ColorList = new enum GraphEdge::Shading[getAtomCount()];
   for (int i=0;i<getAtomCount();i++)
-    ColorList[i] = (enum bond::Shading)0;
+    ColorList[i] = (enum GraphEdge::Shading)0;
   if (flag) {
     // remove bonds that are beyond bonddistance
@@ -1836 +1835 @@
       // apply to all atoms of first component via BFS
       for (int i=getAtomCount();i--;)
-        ColorList[i] = bond::white;
+        ColorList[i] = GraphEdge::white;
       AtomStack->push_front(Binder->leftatom);
       while (!AtomStack->empty()) {
@@ -1842 +1841 @@
         AtomStack->pop_front();
         //Log() << Verbose (3) << "Current Walker is: " << *Walker << "." << endl;
-        ColorList[Walker->getNr()] = bond::black;    // mark as explored
+        ColorList[Walker->getNr()] = GraphEdge::black;    // mark as explored
         *Walker += Translationvector; // translate
         const BondList& ListOfBonds = Walker->getListOfBonds();
@@ -1850 +1849 @@
           if ((*Runner) != Binder) {
             OtherWalker = (*Runner)->GetOtherAtom(Walker);
-            if (ColorList[OtherWalker->getNr()] == bond::white) {
+            if (ColorList[OtherWalker->getNr()] == GraphEdge::white) {
               AtomStack->push_front(OtherWalker); // push if yet unexplored
             }

src/molecule_geometry.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include "Helpers/helpers.hpp"
+#include "atom.hpp"
+#include "Bond/bond.hpp"
+#include "Box.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "config.hpp"
+#include "element.hpp"
+#include "Graph/BondGraph.hpp"
+#include "Helpers/helpers.hpp"
+#include "LinearAlgebra/leastsquaremin.hpp"
 #include "LinearAlgebra/Line.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Plane.hpp"
-
-#include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
-#include "config.hpp"
-#include "element.hpp"
-#include "LinearAlgebra/leastsquaremin.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
-
-#include "Box.hpp"
 
 #include <boost/foreach.hpp>

src/molecule_graph.cpp

@@ -23 +23 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Bond/bond.hpp"
 #include "Box.hpp"
 #include "CodePatterns/Assert.hpp"
@@ -32 +31 @@
 #include "config.hpp"
 #include "element.hpp"
+#include "Graph/BondGraph.hpp"
 #include "Helpers/defs.hpp"
 #include "Helpers/fast_functions.hpp"
@@ -48 +48 @@
   atom **PredecessorList;
   int *ShortestPathList;
-  enum bond::Shading *ColorList;
+  enum GraphEdge::Shading *ColorList;
   std::deque<atom *> *BFSStack;
   std::deque<atom *> *TouchedStack;
@@ -173 +173 @@
   for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
     const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
-    if ((!ListOfBonds.empty()) && ((*ListOfBonds.begin())->Type == bond::Undetermined)) {
+    if ((!ListOfBonds.empty()) && ((*ListOfBonds.begin())->Type == GraphEdge::Undetermined)) {
       DoLog(0) && (Log() << Verbose(0) << "No Depth-First-Search analysis performed so far, calling ..." << endl);
       Subgraphs = DepthFirstSearchAnalysis(BackEdgeStack);
@@ -237 +237 @@
     DoLog(2) && (Log() << Verbose(2) << "Current Unused Bond is " << *Binder << "." << endl);
     // (4) Mark Binder used, ...
-    Binder->MarkUsed(bond::black);
+    Binder->MarkUsed(GraphEdge::black);
     OtherAtom = Binder->GetOtherAtom(Walker);
     DoLog(2) && (Log() << Verbose(2) << "(4) OtherAtom is " << OtherAtom->getName() << "." << endl);
     if (OtherAtom->GraphNr != -1) {
       // (4a) ... if "other" atom has been visited (GraphNr != 0), set lowpoint to minimum of both, go to (3)
-      Binder->Type = bond::BackEdge;
+      Binder->Type = GraphEdge::BackEdge;
       DFS.BackEdgeStack->push_front(Binder);
       Walker->LowpointNr = (Walker->LowpointNr < OtherAtom->GraphNr) ? Walker->LowpointNr : OtherAtom->GraphNr;
@@ -248 +248 @@
     } else {
       // (4b) ... otherwise set OtherAtom as Ancestor of Walker and Walker as OtherAtom, go to (2)
-      Binder->Type = bond::TreeEdge;
+      Binder->Type = GraphEdge::TreeEdge;
       OtherAtom->Ancestor = Walker;
       Walker = OtherAtom;
@@ -504 +504 @@
         if (DoLog(2)) {
           ostream &out = (Log() << Verbose(2));
-          out << ((Binder->Type == bond::TreeEdge) ? "TreeEdge " : "BackEdge ") << *Binder << ": <";
+          out << ((Binder->Type == GraphEdge::TreeEdge) ? "TreeEdge " : "BackEdge ") << *Binder << ": <";
           out << ((Binder->leftatom->SeparationVertex) ? "SP," : "") << "L" << Binder->leftatom->LowpointNr << " G" << Binder->leftatom->GraphNr << " Comp.";
           Binder->leftatom->OutputComponentNumber(&out);
@@ -528 +528 @@
   BFS.PredecessorList = new atom*[AtomCount];
   BFS.ShortestPathList = new int[AtomCount];
-  BFS.ColorList = new enum bond::Shading[AtomCount];
+  BFS.ColorList = new enum GraphEdge::Shading[AtomCount];
   BFS.BFSStack = new std::deque<atom *> (AtomCount);
   BFS.TouchedStack = new std::deque<atom *> (AtomCount);
@@ -535 +535 @@
     BFS.ShortestPathList[i] = -1;
     BFS.PredecessorList[i] = 0;
-    BFS.ColorList[i] = bond::white;
+    BFS.ColorList[i] = GraphEdge::white;
   }
 };
@@ -563 +563 @@
     BFS.PredecessorList[Walker->getNr()] = NULL;
     BFS.ShortestPathList[Walker->getNr()] = -1;
-    BFS.ColorList[Walker->getNr()] = bond::white;
+    BFS.ColorList[Walker->getNr()] = GraphEdge::white;
   }
 };
@@ -602 +602 @@
 #endif
         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
-        if (BFS.ColorList[OtherAtom->getNr()] == bond::white) {
+        if (BFS.ColorList[OtherAtom->getNr()] == GraphEdge::white) {
           BFS.TouchedStack->push_front(OtherAtom);
-          BFS.ColorList[OtherAtom->getNr()] = bond::lightgray;
+          BFS.ColorList[OtherAtom->getNr()] = GraphEdge::lightgray;
           BFS.PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
           BFS.ShortestPathList[OtherAtom->getNr()] = BFS.ShortestPathList[Walker->getNr()] + 1;
@@ -620 +620 @@
       } else {
         DoLog(2) && (Log() << Verbose(2) << "Skipping hydrogen atom " << *OtherAtom << "." << endl);
-        BFS.ColorList[OtherAtom->getNr()] = bond::black;
+        BFS.ColorList[OtherAtom->getNr()] = GraphEdge::black;
       }
 #endif
@@ -627 +627 @@
       }
     }
-    BFS.ColorList[Walker->getNr()] = bond::black;
+    BFS.ColorList[Walker->getNr()] = GraphEdge::black;
     DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " black." << endl);
     if (OtherAtom == BFS.Root) { // if we have found the root, check whether this cycle wasn't already found beforehand
@@ -647 +647 @@
             BFS.PredecessorList[OtherAtom->getNr()] = NULL;
             BFS.ShortestPathList[OtherAtom->getNr()] = -1;
-            BFS.ColorList[OtherAtom->getNr()] = bond::white;
+            BFS.ColorList[OtherAtom->getNr()] = GraphEdge::white;
             // rats ... deque has no find()
             std::deque<atom *>::iterator iter = find(
@@ -734 +734 @@
         OtherAtom = (*Runner)->GetOtherAtom(Walker);
         //Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *Binder << "." << endl;
-        if (BFS.ColorList[OtherAtom->getNr()] == bond::white) {
+        if (BFS.ColorList[OtherAtom->getNr()] == GraphEdge::white) {
           BFS.TouchedStack->push_front(OtherAtom);
-          BFS.ColorList[OtherAtom->getNr()] = bond::lightgray;
+          BFS.ColorList[OtherAtom->getNr()] = GraphEdge::lightgray;
           BFS.PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
           BFS.ShortestPathList[OtherAtom->getNr()] = BFS.ShortestPathList[Walker->getNr()] + 1;
@@ -753 +753 @@
       }
     }
-    BFS.ColorList[Walker->getNr()] = bond::black;
+    BFS.ColorList[Walker->getNr()] = GraphEdge::black;
     //Log() << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl;
   }
@@ -881 +881 @@
       Runner != ListOfBonds.end();
       ++Runner)
-    if ((*Runner)->IsUsed() == bond::white)
+    if ((*Runner)->IsUsed() == GraphEdge::white)
       return ((*Runner));
   return NULL;

src/moleculelist.cpp

@@ -25 +25 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Bond/bond.hpp"
 #include "boundary.hpp"
 #include "Box.hpp"
@@ -34 +33 @@
 #include "config.hpp"
 #include "element.hpp"
+#include "Graph/BondGraph.hpp"
 #include "Helpers/fast_functions.hpp"
 #include "Helpers/helpers.hpp"

src/unittests/AnalysisBondsUnitTest.cpp

@@ -30 +30 @@
 #include "analysis_bonds.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
+#include "element.hpp"
 #include "Graph/BondGraph.hpp"
-#include "element.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"

src/unittests/BondGraphUnitTest.cpp

@@ -31 +31 @@
 
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
+#include "CodePatterns/Log.hpp"
+#include "element.hpp"
 #include "Graph/BondGraph.hpp"
-#include "element.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"

src/unittests/CountBondsUnitTest.cpp

@@ -32 +32 @@
 #include "analysis_bonds.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
+#include "element.hpp"
 #include "Graph/BondGraph.hpp"
-#include "element.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"

src/unittests/ListOfBondsUnitTest.cpp

@@ -29 +29 @@
 #include "World.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
+#include "Bond/bond.hpp"
 #include "element.hpp"
 #include "molecule.hpp"