Re: [Cdk-devel] About semantics of some CDK elements

[<a.s...@ch...>]

The stereo-chemistry concepts I'm aware of are:

1) Chiral atoms (with at least 4 distinct substituents)
2) (E)/(Z) isomerism on double bonds
3) cis/trans isomerism on ring systems
4) Chiral spiro compounds

There might be more...

I think that isomerism types 1), 3) and 4) can be described by defining 
an atom either as (R) or (S) by the Cahn Ingold Prelog priority rules. 
IAtom.getStereoParity() can be used for this.

E/Z isomerism (type 2) cannot use IAtom.getStereoParity(). Rather 
IBond.setStereo() could be used, but with newly defined constants for E 
and Z. Prioritization of the substituents of a double bond is again done 
with the Cahn Ingold Prelog rules.

Now it might not be a trivial task at all to get from the SMILES' way of 
stereo chemistry representation to the IUPAC one.

--Andreas

Stefan Kuhn wrote:
>>> stereo could be present. (As far as I know currenly the SMILES parser
>>> does not handle this situtation. Anyway this is not my question here).
>> Either the parser or the generator does... so the code explains how
>> the mapping is done...
> The generator does, i. e. it generates stereo smiles (needs coordinates for it 
> and wedge bonds), the parser ignores stereo hints.
>>> I would suggest for example new constants for CIS/TRANS double bond
>>> configuration. And accordingly when function getStereoParity() is called
>>> for a double bond with already known configuration, the approriate
>>> constant could be return.
>>> Or of cource this information could be stored as a new property.
>> IAtom.getStereoParity() is really for atoms, I think...
> 
> Right now the smiles generato creates a smiles directly from wedge bonds. I 
> had the idea (but never did it) to have a stereo coding in cdk, which would 
> abstract from the many ways to describe the same situation with wedge bonds. 
> Code from smiles generator could be used for reading that. Other components 
> (e. g. smiles generator) could use that and parsers could create it (much 
> easier than to create a wedge bond "image" (which would be needed right now).
> Not sure if the stereo parity does that. Anybody knows what it is about?
> 
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-- 
Andreas Schüller
PhD student in the research group of Prof. Dr. Gisbert Schneider

Johann Wolfgang Goethe University
Beilstein-endowed Chair for Chemoinformatics
Building B - 3rd floor
Siesmayerstr. 70
60323 Frankfurt am Main
Germany

Tel.: +49 69 798 24879
Fax: +49 69 798 24880
http://www.modlab.de/