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Last change on this file since 266237 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: 2.9 KB

Line
1	INCLUDES = -I$(top_srcdir)/src
2
3	noinst_PROGRAMS = ActOnAllUnitTest AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest ListOfBondsUnitTest MemoryAllocatorUnitTest MemoryUsageObserverUnitTest VectorUnitTest
4
5	TESTS = ActOnAllUnitTest AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest ListOfBondsUnitTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest VectorUnitTest
6	check_PROGRAMS = $(TESTS)
7
8	ActOnAllUnitTest_SOURCES = ActOnAllTest.hpp ActOnAllUnitTest.cpp ActOnAllUnitTest.hpp memoryallocator.hpp
9	ActOnAllUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
10	ActOnAllUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
11	ActOnAllUnitTest_LDADD = ../libmolecuilder.a
12
13	AnalysisCorrelationToPointUnitTest_SOURCES = analysis_correlation.hpp AnalysisCorrelationToPointUnitTest.cpp AnalysisCorrelationToPointUnitTest.hpp
14	AnalysisCorrelationToPointUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
15	AnalysisCorrelationToPointUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
16	AnalysisCorrelationToPointUnitTest_LDADD = ../libmolecuilder.a
17
18	AnalysisCorrelationToSurfaceUnitTest_SOURCES = analysis_correlation.hpp AnalysisCorrelationToSurfaceUnitTest.cpp AnalysisCorrelationToSurfaceUnitTest.hpp
19	AnalysisCorrelationToSurfaceUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
20	AnalysisCorrelationToSurfaceUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
21	AnalysisCorrelationToSurfaceUnitTest_LDADD = ../libmolecuilder.a
22
23	AnalysisPairCorrelationUnitTest_SOURCES = analysis_correlation.hpp AnalysisPairCorrelationUnitTest.cpp AnalysisPairCorrelationUnitTest.hpp
24	AnalysisPairCorrelationUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
25	AnalysisPairCorrelationUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
26	AnalysisPairCorrelationUnitTest_LDADD = ../libmolecuilder.a
27
28	ListOfBondsUnitTest_SOURCES = listofbondsunittest.cpp listofbondsunittest.hpp
29	ListOfBondsUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
30	ListOfBondsUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
31	ListOfBondsUnitTest_LDADD = ../libmolecuilder.a
32
33	VectorUnitTest_SOURCES = defs.hpp helpers.hpp leastsquaremin.hpp memoryallocator.hpp memoryusageobserver.hpp vectorunittest.cpp vectorunittest.hpp vector.hpp verbose.hpp
34	VectorUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
35	VectorUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
36	VectorUnitTest_LDADD = ../libmolecuilder.a
37
38	MemoryAllocatorUnitTest_SOURCES = defs.hpp helpers.hpp memoryallocatorunittest.cpp memoryallocatorunittest.hpp memoryallocator.hpp memoryusageobserver.hpp verbose.hpp
39	MemoryAllocatorUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS) -I..
40	MemoryAllocatorUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
41	MemoryAllocatorUnitTest_LDADD = ../libmolecuilder.a
42
43	MemoryUsageObserverUnitTest_SOURCES = defs.hpp helpers.hpp memoryusageobserverunittest.cpp memoryusageobserverunittest.hpp memoryusageobserver.hpp verbose.hpp
44	MemoryUsageObserverUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
45	MemoryUsageObserverUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
46	MemoryUsageObserverUnitTest_LDADD = ../libmolecuilder.a

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