Re: [Cdk-devel] kekule recognizers: now and later

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

On Mon, Apr 2, 2012 at 2:58 PM, Rajarshi Guha <raj...@gm...> wrote:
> Excellent initiative. Do any readers automatically perform bond
> assignments?

No, I think they do not, and also think they should not. Lego (tm) style.

> If so I assume they will need to be updated.

Instead, they should report where the input file had uncertainty... if
an MDL molfile does not give the bond order between two atoms, but
uses type 4, then the resulting data model should reflect just that.

With this plan, that will be possible.

> Also, I prefer Order.UNKNOWN rather than null

OK, noted.

Meanwhile, Nina++ has helped out great and set up using her Ambit [0]
this great service:

http://apps.ideaconsult.net:8080/ambit2/depict/cdk?search=c2ccc3n%28%5BH%5D%29c1ccccc1c3%28c2%29&smarts=a

This shows various of the algorithms the CDK has to find the location
of double bonds.

Egon

0.http://www.jcheminf.com/content/3/1/18

-- 
Dr E.L. Willighagen
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Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
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