Changeset 872b51 for molecuilder/src/bond.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/bond.hpp (modified) (2 diffs)

molecuilder/src/bond.hpp

@@ -25 +25 @@
 
 /** Bonds between atoms.
- * Class incorporates bonds between atoms in a molecule,
- * used to derive tge fragments in many-body bond order
- * calculations.
+ * 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
+ * hence the molecule. Thus, bonds belong globally to the molecule
+ * (and are free'd there) and only locally to the atom classs.
  */
 class bond {
@@ -41 +43 @@
     enum EdgeType Type;//!< whether this is a tree or back edge
 
-  atom * GetOtherAtom(atom *Atom) const;
-  bond * GetFirstBond();
-  bond * GetLastBond();
+  atom * GetOtherAtom(const atom *Atom) const;
 
   bool MarkUsed(enum Shading color);