Bugs item #3403862, was opened at 2011-09-03 21:17
Message generated for change (Tracker Item Submitted) made by do0gie
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3403862&group_id=40728
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: File Translation
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: David Nunn (do0gie)
Assigned to: Nobody/Anonymous (nobody)
Summary: Mishandling N+ implict Hcounts
Initial Comment:
This is Open Babel 2.3.0, under Mac OS X 10.6.8.
Try the commandline:
% obabel -:'C=[N+]C Radical Cation' -osdf --gen2d
Radical Cation
OpenBabel09031121052D
3 2 0 0 0 0 0 0 0 0999 V2000
1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8660 0.5000 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
M CHG 1 2 1
M END
$$$$
1 molecule converted
Note that no M RAD property is perceived for the nitrogen, though it should be.
Now the commandline:
% obabel ATTACHED_FILE.sdf -o can
c1ccc[n+]c1 Pyridinium
C[N+]=C Iminium
2 molecules converted
Here the bug runs the other way -- the SD file has positively charged nitrogens
(no radicals defined), for which an implicit hydrogen should be perceived, but
the SMILES show the radical form, rather than the expected c1ccc[nH+]c1 and
C[NH+]=C.
-Dave Nunn
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3403862&group_id=40728
------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
