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listofbondsunittest.hpp@ fc1b24

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Last change on this file since fc1b24 was 266237, checked in by Frederik Heber <heber@…>, 16 years ago

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@…>

Property mode set to 100644

File size: 1.1 KB

Line
1	/*
2	* listofbondsunittest.hpp
3	*
4	* Created on: 18 Oct 2009
5	* Author: user
6	*/
7
8	#ifndef LISTOFBONDSUNITTEST_HPP_
9	#define LISTOFBONDSUNITTEST_HPP_
10
11	#include <cppunit/extensions/HelperMacros.h>
12
13	class element;
14	class molecule;
15	class periodentafel;
16
17	/******************************************** Test classes ************************************/
18
19	class ListOfBondsTest : public CppUnit::TestFixture
20	{
21	CPPUNIT_TEST_SUITE( ListOfBondsTest) ;
22	CPPUNIT_TEST ( AddingBondTest );
23	CPPUNIT_TEST ( RemovingBondTest );
24	CPPUNIT_TEST ( RemovingBondsTest );
25	CPPUNIT_TEST ( RemoveAtomTest );
26	CPPUNIT_TEST ( DeleteBondTest );
27	CPPUNIT_TEST ( DeleteAtomTest );
28	CPPUNIT_TEST_SUITE_END();
29
30	public:
31	void setUp();
32	void tearDown();
33	void AddingBondTest();
34	void RemovingBondTest();
35	void RemovingBondsTest();
36	void RemoveAtomTest();
37	void DeleteBondTest();
38	void DeleteAtomTest();
39
40	private:
41
42	molecule *TestMolecule;
43	element *hydrogen;
44	periodentafel *tafel;
45	};
46
47
48	#endif /* LISTOFBONDSUNITTEST_HPP_ */

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source: src/unittests/listofbondsunittest.hpp@ fc1b24

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