Re: [cml/ccml-discuss] 'Either' single stereo bond representation?

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

On Sat, Nov 13, 2010 at 11:36 PM, Dmitry Pavlov <dp...@gg...>wrote:

> Hello all,
>
> I am wondering if the CML format has (or will have)
> the possibility to encode the "wavy" single bonds,
> which usually mean "either" stereo configuration
> on an atom?
>

Thanks for the question and interest.

CML is designed primarily to represent precise knowledge of the chemistry.
The concept of "either" is not universally agreed. It could mean "unknown",
or "a mixture of compunds" or (as often happens) not recorded (which is not
the same as unknown). Itat  could mean "we know that there is only one
configuration at this stereocentre but we don't know what it is". I don't
believe there is agreement in the community about the semantics alythough
the IUPAC group has been working on it.

If you mean "both" then you are describing a mixture of compounds. The
convention that mixtures can be encoded by fuzzy bonds is not easy to
support with software. It is best described by using symbols and we have
done this for some systems and if the community agrees on stereochemistry
may use this approach. (It is not esy to describe a mixture of diasteomers
with several centres).

The concept of "unknown" can be modelled by omitting the information. (JUMBO
would set this to null). There are many other cases where information can be
omitted to the same effect.

You are allowed to create your own conventions as long as they are labelled
with the @convention attribute - this could be used for bondStereo.

the idea of a convention is that everyone agrees it and builds software that
processes it in the same way. If this is actually the case - and there are
validating systems then a case can be made.

please mail again if this is not clear.

>
> Best regards,
>
> Dmitry Pavlov
>
>
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-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069