exception: stereocenters: stereo types of the opposite bonds mismatch
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Karen Karapetyan
Apr 7, 2013, 5:02:16 PM4/7/13
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Could oyu pls exlain this exception:
stereocenters: stereo types of the opposite bonds mismatch
at com.ggasoftware.indigo.Indigo.checkResult(Int32 result)
at com.ggasoftware.indigo.Indigo.loadMolecule(String str)
here is the molecule:
--------------------------
ChEBI
Mrv0541 04191212152D
69 72 0 0 1 0 999 V2000
7.7387 -13.8482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7387 -14.6732 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
7.0242 -13.4357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0242 -15.0857 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.3098 -13.8482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3098 -14.6732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4533 -15.0857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4533 -15.9107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.7387 -16.3232 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.0243 -15.9107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3099 -16.3233 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5955 -15.9109 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.8823 -15.0857 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
9.8823 -15.9107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1677 -14.6732 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.3112 -15.0857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3112 -15.9107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.5967 -14.6732 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
10.5967 -16.3232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0258 -13.8482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0258 -14.6732 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
10.5968 -13.8482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4548 -13.8482 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
13.4548 -14.6732 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
12.7402 -13.4357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.7402 -15.0857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0242 -17.5606 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.3099 -17.1481 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
7.0242 -18.3855 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
6.3097 -18.7978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5955 -17.5605 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
5.5954 -18.3853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7387 -18.7980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7387 -19.6230 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
7.0242 -20.0355 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.1677 -19.6230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4531 -20.0355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4531 -20.8604 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0242 -20.8603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.5129 -15.4472 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8811 -17.1479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.5967 -17.1482 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
9.8822 -17.5606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3112 -17.5607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3112 -18.3857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.5967 -18.7982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0256 -18.7982 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
12.0256 -19.6232 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
11.3111 -20.0357 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
12.7402 -18.3857 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
12.7401 -20.0357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0243 -19.0850 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
9.1614 -21.2929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1614 -22.2514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.7401 -20.8606 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
12.0020 -21.2573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3112 -20.8605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4546 -19.6232 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.8214 -22.6207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.5364 -22.1257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3457 -22.1257 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
13.4593 -21.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0371 -22.9664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0371 -15.4707 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
14.1692 -13.4357 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
14.1692 -15.0857 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
14.8837 -14.6733 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7393 -15.5179 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.3093 -18.0007 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 1 1 0 0 0 0
5 3 1 0 0 0 0
6 5 1 0 0 0 0
2 7 1 1 0 0 0
4 2 1 0 0 0 0
6 4 1 0 0 0 0
10 4 1 0 0 0 0
12 11 2 0 0 0 0
15 13 1 0 0 0 0
7 15 1 0 0 0 0
8 7 2 0 0 0 0
19 17 2 0 0 0 0
13 18 1 0 0 0 0
14 13 1 0 0 0 0
16 21 1 0 0 0 0
18 16 1 0 0 0 0
18 22 1 1 0 0 0
24 23 1 0 0 0 0
25 23 1 0 0 0 0
26 24 1 0 0 0 0
20 25 1 0 0 0 0
21 26 1 0 0 0 0
21 20 1 0 0 0 0
10 9 2 0 0 0 0
11 10 1 0 0 0 0
28 11 1 0 0 0 0
29 27 1 6 0 0 0
28 27 1 6 0 0 0
31 28 1 0 0 0 0
32 30 1 0 0 0 0
32 31 1 0 0 0 0
29 33 1 0 0 0 0
30 29 1 0 0 0 0
37 36 1 0 0 0 0
34 33 1 0 0 0 0
38 37 2 0 0 0 0
34 37 1 0 0 0 0
34 35 1 1 0 0 0
39 35 1 0 0 0 0
13 40 1 1 0 0 0
31 41 1 1 0 0 0
42 19 1 0 0 0 0
14 19 1 0 0 0 0
45 44 2 0 0 0 0
42 44 1 0 0 0 0
42 43 1 1 0 0 0
48 47 1 0 0 0 0
45 47 1 0 0 0 0
46 45 1 0 0 0 0
47 50 1 1 0 0 0
48 51 1 0 0 0 0
29 52 1 1 0 0 0
53 38 1 0 0 0 0
54 53 2 0 0 0 0
55 51 1 0 0 0 0
56 55 1 0 0 0 0
48 49 1 6 0 0 0
57 49 1 0 0 0 0
58 51 2 0 0 0 0
59 54 1 0 0 0 0
60 59 2 0 0 0 0
61 60 1 0 0 0 0
56 61 1 0 0 0 0
55 62 1 6 0 0 0
61 63 1 6 0 0 0
21 64 1 1 0 0 0
23 65 1 1 0 0 0
24 66 1 6 0 0 0
67 66 1 0 0 0 0
2 68 1 6 0 0 0
28 69 1 1 0 0 0
M END
Mikhail Rybalkin
Apr 8, 2013, 8:36:42 AM4/8/13
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I marked a stereocenter that depicted in a wrong way. We can append an atom index in the exception message.
We follow guideline described in the Graphical Representation of Stereochemical Configuration document. This case is described on the page 20 in the paragraph ST-1.1.10.
Karen Karapetyan
Apr 9, 2013, 10:35:23 AM4/9/13
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Thanks. Appending atom index would help a lot.
Actually chemical validation is getting more and more attention and if indigo could address validation in systematic way that could greatly be popular with users.
By systematic I mean not throwing exception but letting user to access all issues with record by special chemical validation method(s). Issues can include stereo ambiguity, unknown atoms, crazy charge or valency, query bonds/atoms,etc.
Mikhail Rybalkin
Apr 19, 2013, 4:04:57 PM4/19/13
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Hi Ken,
I added an atom index to the exception message in the Indigo 1.1.10. Now it would be easier to locate invalid stereocenters.
Problem with chemical validation is that it is not clear how to fix such problems automatically. If user forgot to mark stereobonds correctly it is not clear whether we should ignore such stereocenter or not...
Best regards,
Mikhail
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