Am I confused, or is this just wrong? These two SMILES should be the
identical molecule:
c1ncccc1
c1[n]cccc1
The first uses valence rules to deduce that there is no H on the nitrogen.
The second specifically says the same thing. Both should thus be the
identical molecule. However...
$ echo "[n]1ccccc1" | obabel -i smi -o can
c1ccc[n]c1
$ echo "n1ccccc1" | obabel -i smi -o can
c1cccnc1
If you print out the SDF, you can see the problem: the first form of the
SMILES with the [n] is marked as a radical:
$ echo "[n]1ccccc1" | obabel -i smi -o sdf
...
M RAD 1 1 2
M END
$$$$
Am I missing something, or should this be filed as a bug?
Thanks,
Craig
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