source: tests/Fragmentations/Fragmenting/phenanthrene/pre/phenanthrene.pdb@ bc4be2

Action_Thermostats
Last change on this file since bc4be2 was ec7511, checked in by Frederik Heber <heber@…>, 12 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: 3.7 KB
Line 
1COMPND UNNAMED
2AUTHOR GENERATED BY OPEN BABEL 2.3.0
3HETATM 1 C LIG 1 29.492 -19.399 0.000 1.00 0.00 C
4HETATM 2 C LIG 1 30.702 -18.698 0.000 1.00 0.00 C
5HETATM 3 C LIG 1 29.489 -16.601 0.000 1.00 0.00 C
6HETATM 4 C LIG 1 30.699 -17.302 0.000 1.00 0.00 C
7HETATM 5 C LIG 1 31.911 -16.603 0.000 1.00 0.00 C
8HETATM 6 C LIG 1 31.912 -15.205 0.000 1.00 0.00 C
9HETATM 7 C LIG 1 30.701 -14.505 0.000 1.00 0.00 C
10HETATM 8 C LIG 1 29.490 -15.203 0.000 1.00 0.00 C
11HETATM 9 C LIG 1 28.275 -18.698 0.000 1.00 0.00 C
12HETATM 10 C LIG 1 28.275 -17.296 0.000 1.00 0.00 C
13HETATM 11 C LIG 1 27.061 -16.595 0.000 1.00 0.00 C
14HETATM 12 C LIG 1 25.847 -17.296 0.000 1.00 0.00 C
15HETATM 13 C LIG 1 25.847 -18.698 0.000 1.00 0.00 C
16HETATM 14 C LIG 1 27.061 -19.399 0.000 1.00 0.00 C
17HETATM 15 H LIG 1 29.493 -20.431 0.000 1.00 0.00 H
18HETATM 16 H LIG 1 31.597 -19.213 0.000 1.00 0.00 H
19HETATM 17 H LIG 1 32.804 -17.120 0.000 1.00 0.00 H
20HETATM 18 H LIG 1 32.806 -14.690 0.000 1.00 0.00 H
21HETATM 19 H LIG 1 30.702 -13.473 0.000 1.00 0.00 H
22HETATM 20 H LIG 1 28.597 -14.686 0.000 1.00 0.00 H
23HETATM 21 H LIG 1 27.061 -15.563 0.000 1.00 0.00 H
24HETATM 22 H LIG 1 24.953 -16.780 0.000 1.00 0.00 H
25HETATM 23 H LIG 1 24.953 -19.214 0.000 1.00 0.00 H
26HETATM 24 H LIG 1 27.061 -20.431 0.000 1.00 0.00 H
27CONECT 1 9 2 15
28CONECT 2 1 4 16
29CONECT 3 8 10 4
30CONECT 4 5 2 3
31CONECT 5 4 6 17
32CONECT 6 5 7 18
33CONECT 7 6 8 19
34CONECT 8 7 3 20
35CONECT 9 1 10 14
36CONECT 10 3 9 11
37CONECT 11 10 12 21
38CONECT 12 11 13 22
39CONECT 13 12 14 23
40CONECT 14 13 9 24
41CONECT 15 1
42CONECT 16 2
43CONECT 17 5
44CONECT 18 6
45CONECT 19 7
46CONECT 20 8
47CONECT 21 11
48CONECT 22 12
49CONECT 23 13
50CONECT 24 14
51MASTER 0 0 0 0 0 0 0 0 24 0 24 0
52END
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