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coronene.pdb

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Candidate_v1.6.1

Last change on this file was ec7511, checked in by Frederik Heber <heber@…>, 11 years ago

FIX: CyclicStructureAnalysis falsely used DFS, skipped some cycles.

FIX: CyclicStructureAnalysis did use DFS instead of BFS for finding cycles. Note that CyclicStructureAnalysis with coronene would find supercycles and not the smaller interconnected ones.
FIX: Cycles were skipped when all bonds marked cyclic, not enough. In interconnected aromatic rings, bonds may very well be marked as cyclic from earlier extraction of cycles and yet the specific cycle might not have been found yet (e.g. coronene). In this case we now check whether this particular cycle has already been extracted and only skip if so.
TESTFIX: added new fragmentation regression tests on some metallic systems.
this is mainly for regression on bond graph detection and cycle analysis.

Property mode set to 100644

File size: 5.5 KB

Rev	Line
[ec7511]	1	COMPND UNNAMED
	2	AUTHOR GENERATED BY OPEN BABEL 2.3.0
	3	HETATM 1 C LIG 1 16.170 -15.750 0.000 1.00 0.00 C
	4	HETATM 2 C LIG 1 16.170 -17.150 0.000 1.00 0.00 C
	5	HETATM 3 C LIG 1 17.382 -17.850 0.000 1.00 0.00 C
	6	HETATM 4 C LIG 1 18.595 -17.150 0.000 1.00 0.00 C
	7	HETATM 5 C LIG 1 18.595 -15.750 0.000 1.00 0.00 C
	8	HETATM 6 C LIG 1 17.382 -15.050 0.000 1.00 0.00 C
	9	HETATM 7 C LIG 1 17.382 -13.650 0.000 1.00 0.00 C
	10	HETATM 8 C LIG 1 16.170 -12.950 0.000 1.00 0.00 C
	11	HETATM 9 C LIG 1 14.958 -13.650 0.000 1.00 0.00 C
	12	HETATM 10 C LIG 1 14.958 -15.050 0.000 1.00 0.00 C
	13	HETATM 11 C LIG 1 13.745 -15.750 0.000 1.00 0.00 C
	14	HETATM 12 C LIG 1 13.745 -17.150 0.000 1.00 0.00 C
	15	HETATM 13 C LIG 1 14.958 -17.850 0.000 1.00 0.00 C
	16	HETATM 14 C LIG 1 14.957 -19.250 0.000 1.00 0.00 C
	17	HETATM 15 C LIG 1 16.170 -19.950 0.000 1.00 0.00 C
	18	HETATM 16 C LIG 1 17.382 -19.250 0.000 1.00 0.00 C
	19	HETATM 17 C LIG 1 18.595 -19.950 0.000 1.00 0.00 C
	20	HETATM 18 C LIG 1 19.807 -19.250 0.000 1.00 0.00 C
	21	HETATM 19 C LIG 1 19.807 -17.850 0.000 1.00 0.00 C
	22	HETATM 20 C LIG 1 21.020 -17.150 0.000 1.00 0.00 C
	23	HETATM 21 C LIG 1 21.020 -15.750 0.000 1.00 0.00 C
	24	HETATM 22 C LIG 1 19.807 -15.050 0.000 1.00 0.00 C
	25	HETATM 23 C LIG 1 19.807 -13.650 0.000 1.00 0.00 C
	26	HETATM 24 C LIG 1 18.595 -12.950 0.000 1.00 0.00 C
	27	HETATM 25 H LIG 1 16.170 -11.918 0.000 1.00 0.00 H
	28	HETATM 26 H LIG 1 14.064 -13.134 0.000 1.00 0.00 H
	29	HETATM 27 H LIG 1 12.851 -15.234 0.000 1.00 0.00 H
	30	HETATM 28 H LIG 1 12.851 -17.666 0.000 1.00 0.00 H
	31	HETATM 29 H LIG 1 14.064 -19.766 0.000 1.00 0.00 H
	32	HETATM 30 H LIG 1 16.170 -20.982 0.000 1.00 0.00 H
	33	HETATM 31 H LIG 1 18.595 -20.982 0.000 1.00 0.00 H
	34	HETATM 32 H LIG 1 20.701 -19.766 0.000 1.00 0.00 H
	35	HETATM 33 H LIG 1 21.914 -17.666 0.000 1.00 0.00 H
	36	HETATM 34 H LIG 1 21.914 -15.234 0.000 1.00 0.00 H
	37	HETATM 35 H LIG 1 20.701 -13.134 0.000 1.00 0.00 H
	38	HETATM 36 H LIG 1 18.595 -11.918 0.000 1.00 0.00 H
	39	CONECT 1 2 6 10
	40	CONECT 2 1 3 13
	41	CONECT 3 2 4 16
	42	CONECT 4 3 5 19
	43	CONECT 5 4 6 22
	44	CONECT 6 5 1 7
	45	CONECT 7 6 8 24
	46	CONECT 8 7 9 25
	47	CONECT 9 8 10 26
	48	CONECT 10 9 1 11
	49	CONECT 11 10 12 27
	50	CONECT 12 11 13 28
	51	CONECT 13 12 2 14
	52	CONECT 14 13 15 29
	53	CONECT 15 14 16 30
	54	CONECT 16 15 3 17
	55	CONECT 17 16 18 31
	56	CONECT 18 17 19 32
	57	CONECT 19 18 4 20
	58	CONECT 20 19 21 33
	59	CONECT 21 20 22 34
	60	CONECT 22 21 5 23
	61	CONECT 23 22 24 35
	62	CONECT 24 23 7 36
	63	CONECT 25 8
	64	CONECT 26 9
	65	CONECT 27 11
	66	CONECT 28 12
	67	CONECT 29 14
	68	CONECT 30 15
	69	CONECT 31 17
	70	CONECT 32 18
	71	CONECT 33 20
	72	CONECT 34 21
	73	CONECT 35 23
	74	CONECT 36 24
	75	MASTER 0 0 0 0 0 0 0 0 36 0 36 0
	76	END

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source: tests/Fragmentations/Fragmenting/coronene/pre/coronene.pdb

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