Re: [Cdk-devel] RFE: On atom parities

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

At 11:29 01/06/2004 +0200, E.L. Willighagen wrote:
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>On Tuesday 01 June 2004 11:15, Peter Murray-Rust wrote:
> > At 10:27 01/06/2004 +0200, E.L. Willighagen wrote:
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> > >Let's address stereochemistry in CDK:
> > >
> > >Take this CML bit:
> > >
> > ><atom id="a1" elementType="O">
> > >   <atomParity atomRefs4="a3 a7 a2 a4">1</atomParity>
> > ></atom>
> >
> > Valid CML - unusual chemistry if a1 is bonded to these ligands. Was it in
> > my docs - in which case I should change it
>
>Yes, it comes from Jumbo4.4_cvs: components/examples/atom1.xml
>
>But, I don't understand what is wrong with it... The missing bond info? Lack
>of coordinates?

Only that it is a four-coordinate stereogenic oxygen which would be unusual 
although it can occur in metal complexes

P.


Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069