Changeset 872b51 for molecuilder/src/molecule.hpp

Timestamp:

Oct 18, 2009, 2:51:38 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

77894f

Parents:

b0ee98

git-author:

Frederik Heber <heber@…> (10/18/09 14:15:37)

git-committer:

Frederik Heber <heber@…> (10/18/09 14:51:38)

Message:

Huge refactoring: molecule::ListOfBondsPerAtom and molecule::NumberOfBondsPerAtom removed, atom::ListOfBonds introduced. Unit Test for ListOfBonds manipulation introduced.

• changes to class atom:
  • ~atom(): removes all bonds it is part of and unlink()s
  • new functions: CountBonds() - counts bonds times BondDegree, OutputGraphInfo() - graph data is output, OutputComponentNumber() - output of component numbers, OutputAdjacency() - indices of this and its neighbours, CorrectBondDegree() - corrects bond degree incrementally (by at most one) -- all since ListOfBonds is now local info
  • OutputBondOfAtom() - does not need ListOfBondsPerAtom, ... as ListOfBonds is now local info
  • new functions for ListOfBonds access: RegisterBond(), UnregisterBond(), UnregisterAllBonds() (the latter only remove from the list, do not delete, as molecule still has a global list of all bonds and does deletion.)

• changes to class bond:
  • ~bond() uses unlink(), uses UnregisterBond() on leftatom and rightatom
  • removed unused bond::GetFirstBond() and bond::GetLastBond()
  • GetOtherAtom() has now const parameter

• changes to builder.cpp: removed CreateListOfBondsPerAtom() calls, as the creation of the global arrays is not necessary anymore

• changes to LinkedCell: LinkedCell::CheckBounds(int[NDIM]) does not admonish out of bonds as this is not desired for the local offset which may become out of bounds.

• changes to lists.hpp templates: BUGFIX: unlink() now sets ->next and ->previous to NULL, cleanup() uses removedwithoutcheck()

• new templates for molecule.hpp: SumPerAtom() allows for summation of the return value of atom:...() member fiunctions. This is needed e.g. for atom::CorrectBondDegree()

• changes to MoleculeListClass:
  • changes due to ListOfBondsPerAtom -> atom::ListOfBonds: AddHydrogenCorrection(), FillBondStructureFromReference()

• changes to class molecule:
  • changes due to ListOfBondsPerAtom -> atom::ListOfBonds: GuesstimateFragmentCount(), FragmentMolecule(), FillSPListandLabelVertices(), ScanForPeriodicCorrection(), DeterminePeriodicCenter(), CyclicStructureAnalysis(), InitComponentNumbers(), FindNextUnused(), CheckAdjacencyFileAgainstMolecule(), PickLocalBackEdges(), BreadthFirstSearchAdd(), BuildInducedSubgraph(), CheckForConnectedSubgraph(), molecule(), ~molecule(), AddHydrogenReplacementAtom(), RemoveBonds(), OutputListOfBonds(), removed CreateListOfBondsPerAtom()
  • due to removal of CreateListOfBonds(): FragmentMolecule(), CreateAdjacencyListFromDbondFile(), CreateAdjacencyList(), SetNextComponentNumber()
  • ActOnAllAtoms() used: CreateAdjacencyList() - uses atom::OutputBondOfAtom(), StoreAdjacencyToFile() - uses atom::OutputAdjacency(),
  • SumPerAtom() used: CorrectBondDegree() - uses atom::CorrectBondDegree(),
  • function removed: molecule::CountAtomsBonds() - shifted to atom::CountBonds(), OutputComponentNumber() - shifted to atom::OutputComponentNumber()
  • CountCyclicBonds() - manipulates molecule::NoCyclicBonds directly.
  • rewritten DepthFirstSearchAnalysis() - refactored to CyclicBondAnalysis(), OutputGraphInfoPerAtom(), OutputGraphInfoPerBond()
  • rewritten RemoveAtom() - uses RemoveBonds()
  • FIX: rewritten CleanupMolecule() - cleanup was wrong order, now is first bonds, then atoms
  • rewritten BreadthFirstSearchAdd() - uses molecule::CopyBond() (equal code was present multiple(!) times before)
  • new functions CyclicBondAnalysis(), OutputGraphInfoPerAtom(), OutputGraphInfoPerBond(), CopyBond()

• New UnitTest for ListOfBonds:
  • tests AddBond(), RemoveAtom(), RemoveBond(), RemoveBonds() and simple deletion of atoms or bonds, where afterwards chain lists of bonds should remain intact.

Signed-off-by: Frederik Heber <heber@…>

File:

• molecuilder/src/molecule.hpp (modified) (6 diffs)

molecuilder/src/molecule.hpp

@@ -86 +86 @@
     bond *first;        //!< start of bond list
     bond *last;         //!< end of bond list
-    bond ***ListOfBondsPerAtom; //!< pointer list for each atom and each bond it has
     int MDSteps;        //!< The number of MD steps in Trajectories
-    int *NumberOfBondsPerAtom;  //!< Number of Bonds each atom has
     int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
     int BondCount;          //!< number of atoms, brought up-to-date by CountBonds()
@@ -190 +188 @@
   template <typename T> void SetAtomValueToIndexedArray ( T *array, int element::*index, T atom::*value );
 
+  template <typename res> res SumPerAtom(res (atom::*f)() );
+  template <typename res> res SumPerAtom(res (atom::*f)() const );
+  template <typename res> res SumPerAtom(res (atom::*f)() ) const;
+  template <typename res> res SumPerAtom(res (atom::*f)() const ) const;
+  template <typename T, typename res> res SumPerAtom(res (atom::*f)(T) , T t );
+  template <typename T, typename res> res SumPerAtom(res (atom::*f)(T) const, T t );
+  template <typename T, typename res> res SumPerAtom(res (atom::*f)(T) , T t ) const;
+  template <typename T, typename res> res SumPerAtom(res (atom::*f)(T) const, T t ) const;
+
   /// remove atoms from molecule.
   bool AddAtom(atom *pointer);
@@ -199 +206 @@
   atom * AddCopyAtom(atom *pointer);
   bool AddXYZFile(string filename);
-  bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem);
+  bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
   bond * AddBond(atom *first, atom *second, int degree = 1);
   bool RemoveBond(bond *pointer);
@@ -247 +254 @@
   void CreateAdjacencyListFromDbondFile(ofstream *out, ifstream *output);
   void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
-  void CreateListOfBondsPerAtom(ofstream *out);
   int CorrectBondDegree(ofstream *out);
   void OutputBondsList(ofstream *out);
-  int CountAtomsBonds(int nr);
+  void CyclicBondAnalysis();
+  void OutputGraphInfoPerAtom(ofstream *out);
+  void OutputGraphInfoPerBond(ofstream *out);
 
 
@@ -260 +268 @@
   void SetNextComponentNumber(atom *vertex, int nr);
   void InitComponentNumbers();
-  void OutputComponentNumber(ofstream *out, atom *vertex);
   void ResetAllBondsToUnused();
   void ResetAllAtomNumbers();
@@ -266 +273 @@
   bool CheckForConnectedSubgraph(ofstream *out, KeySet *Fragment);
   string GetColor(enum Shading color);
+  bond * CopyBond(atom *left, atom *right, bond *CopyBond);
+
 
   molecule *CopyMolecule();