Re: [Cdk-devel] marking atom explicitly aromatic

[Egon W. <ego...@gm...>]

On Sun, Feb 13, 2011 at 3:39 PM, Andrew Dalke <da...@da...> wrote:
> On Feb 13, 2011, at 4:29 PM, Egon Willighagen wrote:
>> I said SMILES, not OpenSMILES :)
>
> True. But then again, CDK doesn't exactly implement SMILES nor OpenSMILES. :)

It tries the first... bug reports welcome... I've seen so many for
SMILES... we solved many know bugs, but I'd be the last to say, there
are none left. (CDK community: if someone is interested in working on
the parser... it doesn't have a maintainer.)

> I was curious so I looked up the Daylight documentation. It says
>
>   single and aromatic bonds may always be omitted
>
> and
>
>   Aromaticity must be deduced in a system such as SMILES
>
> so what I said definitely is not part of SMILES.
>
> But it also says:
>
>   it is not necessary to enter any structure as aromatic if the
>   user prefers to enter an aliphatic (Kekulé-like) structure
>
> I take from that the implication that people enter structures, while
> my use case is for when structures entered by other software.

Yeah, it's this kind of ambiguity why I like OpenSMILES, as that
project tries to iron out those missing details...

Then again, these things are exactly why I personally favor explicit
formats. Just say what you mean. CML comes closest.

Egon


-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet
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