Andrew Dalke wrote:
> On Oct 29, 2009, at 7:49 PM, Chris Swain wrote:
>> The SMILES definition of aromaticity would seem to be an excellent
>> solution.
>
> Except when it isn't. That's why different people and different
> software have different aromaticity models.
>
> I wrote some about this in
> http://www.dalkescientific.com/writings/diary/archive/2007/11/30/
> opensmiles_and_aromaticity.html
>
> and pointed out that OpenEye's OEAssignAromaticFlags implements "the
> Daylight, Tripos, MMFF and MDL definitions."
Right, these are all good points. But we're not talking about OpenBabel 3, or
the details of the OpenSMILES spec. We're talking about OpenBabel 2, which has
some serious flaws, i.e. aromaticity code that's just plain wrong, and we
already know we're not going to embark on a huge new cycle of development for
OpenBabel 2.
I need certain things fixed, and I have to do it now, using OpenBabel 2. I
need a pragmatic, short-term solution. The questions I'm asking are:
- Whether there's any interest by others in the work I'll be doing
- Whether the current aromaticity detection in OpenBabel is bad
science
I don't have an opinion on either, I'm just asking.
Craig
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