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testsuite-selection-all-atoms-of-molecule.at@ 61749d1

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Last change on this file since 61749d1 was 49c059, checked in by Frederik Heber <heber@…>, 14 years ago

Moved DepthFirstSearchAnalysis into functor in Graph/.

Smaller fixes:

molecule::CorrectBondDegree() - does not rely on BondCount which was not necessary anyway.

DFS does not copy atoms or molecules anymore but reinitiates the current molecule structure with present atoms, used new class ConnectedSubgraph for that. New functions:
- UpdateMoleculeStructure() - reinstantiates molecules.
- getMoleculeStructure() - puts molecules into chained list.
adapted because of that:
- DepthFirstSearchAction: uses DFS and CSA functors, also UpdateMoleculeStructure() such that CSA has current structure.
- FragmentationAction: assumes connectivity fully present, DFS created.
- SubgraphDissectionAction: uses DFS and UpdateMoleculeStructure().
- molecule::FragmentMolecule(): no more DFS, instead DFS has to happen beforehand and is given as parameter, used to obtain chained list for compatibility for the moment.
DepthFirstSearchAnalysis::SetNextComponentNumber() bugfix due to wrong assert.

TESTFIXES:

Fragmentation and regression test Fragmentation/FragmentMolecule: FragmentationAction now needs SubgraphDissectionAction beforehand.
shifted id (down by one) due to non-copying (before: one big molecule, copied and split up system started at 1, now it starts at 0):
- (Un)Selection/Atoms/AllAtomsOfMolecule
- Analysis/SurfaceCorrelation
- (Un)Selection/Molecules/MoleculeById (also renamed post-files accordingly)
- (Un)Selection/Molecules/MoleculeByName

Property mode set to 100644

File size: 5.2 KB

Rev	Line
[512f85]	1	### 4. (un)select all atoms of molecule
	2
	3	AT_SETUP([Selection - All atoms of selected molecules])
	4	AT_KEYWORDS([selection])
	5	file=molecule1.xyz
[b9bfa6]	6	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	7	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 0 --select-molecules-atoms -r], 0, [stdout], [stderr])
[b9bfa6]	8	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
	9	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	10	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 0 --select-molecules-atoms --undo -r], 0, [stdout], [stderr])
[b9bfa6]	11	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz], 0, [ignore], [ignore])
	12	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	13	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 0 --select-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
[b9bfa6]	14	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
[512f85]	15	file=molecule0.xyz
[b9bfa6]	16	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	17	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 1 --select-molecules-atoms -r], 0, [stdout], [stderr])
[b9bfa6]	18	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
	19	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	20	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 1 --select-molecules-atoms --undo -r], 0, [stdout], [stderr])
[b9bfa6]	21	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz], 0, [ignore], [ignore])
	22	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	23	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-molecule-by-id 1 --select-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
[b9bfa6]	24	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
[512f85]	25	AT_CLEANUP
	26
	27	AT_SETUP([Unselection - All atoms of selected molecules])
	28	AT_KEYWORDS([selection])
	29	file=molecule0.xyz
[b9bfa6]	30	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	31	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 0 --unselect-molecules-atoms -r], 0, [stdout], [stderr])
[b9bfa6]	32	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
	33	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	34	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 0 --unselect-molecules-atoms --undo -r], 0, [stdout], [stderr])
[b9bfa6]	35	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/empty.xyz], 0, [ignore], [ignore])
	36	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	37	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 0 --unselect-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
[b9bfa6]	38	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
[512f85]	39	file=molecule1.xyz
[b9bfa6]	40	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	41	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 1 --unselect-molecules-atoms -r], 0, [stdout], [stderr])
[b9bfa6]	42	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
	43	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	44	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 1 --unselect-molecules-atoms --undo -r], 0, [stdout], [stderr])
[b9bfa6]	45	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/empty.xyz], 0, [ignore], [ignore])
	46	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/pre/test.xyz $file], 0)
[49c059]	47	AT_CHECK([../../molecuilder -i $file -v 3 -I --select-all-atoms --select-molecule-by-id 1 --unselect-molecules-atoms --undo --redo -r], 0, [stdout], [stderr])
[b9bfa6]	48	AT_CHECK([diff -I '.Created by molecuilder.' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Selection/Atoms/AllAtomsOfMolecule/post/$file], 0, [ignore], [ignore])
[512f85]	49	AT_CLEANUP

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