Re: [Cdk-devel] Coordination bonds

[Stefan K. <ste...@eb...>]

On Tuesday 08 December 2009 13:41:52 Miguel Rojas Cherto wrote:
> On Mon, Dec 7, 2009 at 5:02 PM, Stefan Kuhn <ste...@eb...> wrote:
> > Hi all,
> > do we have support for coordination bonds in CDK? If not, how could these
> > be introduced? As a property on bonds? From my short wikipedia reading I
> > get the impression it is very similar to "normal" bonds, so it might be
> > appropriate to have them as such with a property. Any thoughts?
>
> Coordinates bonds are lone pare electrons (which normally doesn't
> participate in bonding atoms) linking to a positively charged atom.
> CDK described lone pair electrons == org.openscience.cdk.LonePair, But
> LonePair class only can accept at the moment one atom. It can not form
> a link between two atoms.
And LonePair actually extends ElectronContainer, as does the Bond. This sounds 
like an extension of LonePair to LonePairBond or CoordinationBond or whatever 
the name is the right thing to do?
Stefan
>
> Maybe it could be extended to accept two atoms to form a bond interface!
>
> Cheers,
>  Miquel
>
> --
> Miguel Rojas Cherto
> Netherlands Metabolomics Centre
> Analytical Biosciences
> Leiden University
> Einsteinweg 55
> NL-2333 CC Leiden
> tel :  +31 715276326
> fax:  +31 715274277
>
> Mail: m....@la...
> http://abs.lacdr.gorlaeus.net
> www.metabolomicscentre.nl



-- 
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
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