Re: [Cdk-devel] Difference in bond between undefined and undefined ?

[Peter Murray-R. <pm...@ca...>]

At 15:20 14/03/2003 +0100, Stefan Kuhn wrote:
>Hi developers,
>I just made the MDLWriter to write chiralities and I discovered that there
>seems to be no difference between the ordinary bond and the undefined
>chiraltiy, i. e. the swung dash (or no value for this, to put it another
>way). Did I oversee it or is it not there ? Should we have a value for
>undefined=3Dswung dash in CDKConstants (and use it) ?
>Cheers
>Stefan
MDL has a value of 4 =3D Either. It depends how you interpret "either". (I=
 am=20
not sure what you mean by "swung bond").

This is a difficult area and is discussed at length recently in:

http://www.angelfire.com/sc3/iupacstructures/

I would encourage CDK to use an abstraction based on these discussions as=20
the starting point.  My opinion is that chirality should be based on atoms=
=20
rather than bonds as the latter (a) require 2D coordinates and (b) are=20
often very poorly represent ed in diagrams. There is a problem for=20
*publishers* who have to manage graphical representations but this is not=20
the main emphasis of CDK.

Best

P.


>--
>Stefan Kuhn M. A.
>Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
>Z=C3=BClpicher Str. 47, 50674 Cologne
>Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-5092
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