On 11/22/10 2:51 PM, Geoffrey Hutchison wrote:
>> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in
>> such way that the bond orders are no longer dependent on the way the
>> molecule was entered? For example, the two smiles representations of the
>> indole ring, N1C=CC2=C1C=CC=C2 and N1C=CC2=CC=CC=C12, lead to differences in
>> the internal bond orders and this has influence on the aromaticity
>> perception.
>
> Are you sure you're using 2.3 release? I just tried these two smiles and asked
> for canonical SMILES and got the same (correct) answers. We fixed a *lot* of
> Kekulization bugs prior to release, so please make sure you're using 2.3
> branch or 2.3.0 release.
>
> [ghutc...@geoffh-desktop] openbabel: echo "N1C=CC2=CC=CC=C12" | babel -ismi
> -ocan
> c1ccc2c(c1)[nH]cc2
> [ghutc...@geoffh-desktop] openbabel: echo "N1C=CC2=C1C=CC=C2" | babel -ismi
> -ocan
> c1ccc2c(c1)[nH]cc2
I don't have Hans' original post but I think he was asking a different
question. His problem was something like this:
1. Read in a SMILES (the indole)
2. Delete the four atoms of the benzene ring that
aren't part of the other ring.
3. Ask if the other ring is aromatic.
It appears that OpenBabel retains the original single/double bond assignment
and uses that to determine aromaticity of the remaining part of the molecule
after atoms are deleted. But depending on the original Kekule assignment of
bonds, the bond that's common to both rings might be single or double. Once
you remove the rest of the benzene ring, the remaining ring may be either
aromatic or not aromatic.
Craig
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