Bugs item #3481603, was opened at 2012-01-30 03:34
Message generated for change (Tracker Item Submitted) made by baoilleach
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Category: File Translation
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Noel O'Boyle (baoilleach)
Assigned to: Nobody/Anonymous (nobody)
Summary: Missing stereo when expanding alias
Initial Comment:
>From marcolipp...@gmail.com nopenbabel-discuss:
Hi,
I am encountering a problem when asking OpenBabel to generate an InChI from
a molecule which has an alias bonded through a wedge/hash bond... It seems
to be missing the wedge/bond after expanding the alias...
Here is an example of what I mean:
OpenBabel01241222313D
20 21 0 0 0 0 0 0 0 0999 V2000
-3.2672 1.9552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.4572 0.9403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9562 -4.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7871 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1816 -0.9104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.4572 -1.0299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0564 0.9403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0125 -1.9254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5553 -2.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7662 -1.0597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9562 -2.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1566 -1.3582 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.4342 3.6269 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
-1.0334 1.6269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.5783 0.6418 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
5.0000 -1.3582 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
-3.4342 -2.3433 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.0334 -4.3433 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3674 -4.3433 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.0000 -5.3284 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 7 2 0 0 0 0
1 13 1 0 0 0 0
2 6 2 0 0 0 0
3 4 1 0 0 0 0
3 11 1 0 0 0 0
3 20 1 1 0 0 0
4 19 1 0 0 0 0
5 7 1 0 0 0 0
5 8 1 0 0 0 0
5 17 2 0 0 0 0
6 17 1 0 0 0 0
7 14 1 0 0 0 0
8 12 1 0 0 0 0
8 18 2 0 0 0 0
9 10 1 0 0 0 0
9 12 1 1 0 0 0
9 19 1 0 0 0 0
10 11 1 0 0 0 0
10 15 1 6 0 0 0
11 16 1 1 0 0 0
A 13
OMe
A 15
OAc
A 16
OAc
A 20
OAc
M END
The generated InChI is
InChI=1S/C18H22N2O10/c1-8(21)28-12-7-27-18(16(30-10(3)23)15(12)29-9(2)22)20-17(25)13-14(24)11(26-4)5-6-19-13/h5-6,12,15-16,18,24H,7H2,1-4H3,(H,20,25)/t12?,15?,16?,18-/m1/s1
Am I missing something ?
Thanks !
Marco
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