Bugs item #3403862, was opened at 2011-09-03 21:17
Message generated for change (Tracker Item Submitted) made by do0gie
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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
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