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

[Dmitry P. <dp...@gg...>]

Hello Peter,

Thank you for your answer.

The origin of my question was primarily the support
of the CML format in the "inchi-1" utility.
Basically, I need to process structures represented
as Molfiles and (the same) structures represented
as CML files and I need to be sure that the results
will match.

So far I have fed Molfiles to this utility.
As far as I have learned, it does recognize
"undefined" atom stereo if no stereo bonds are drawn,
and marking a bond as "either" has no effect -- the
InChI code is the same, and will be the same for
the CML file with unmarked stereo bonds.
So yes, "either" bonds are not useful in this case.
However, there are other cases:

1) Representing undefined stereo in 3D structures.
The InChI Manual says: "[...] (wavy) bonds in the
3-dimensional case still provide “unknown” stereochemistry
even if the coordinates allow calculation of the sp
parity. I wonder what is your opinion about this:
maybe the "atomParity=0" CML property means the
same in the 3D case? I am not really sure.

2) Connecting "either" bonds to a stereoatom
that already has "up" and/or "down" bonds
connected discards the effect of these bonds
and makes the stereo configuration undefined.
I am not sure that this use case makes any sense,
though.

3) An "either" bond connected to a cis-trans
double bond makes this bond "undefined cis-trans".
This makes perfect sense for Molfiles, and I
wonder if there is a way (for instance,
setting "bondStereo=0" or otherwise) to represent
"undefined cis-trans" bond for 2D structures in
the CML format.


With best regards,

Dmitry Pavlov




On 11/14/2010 04:08 AM, Peter Murray-Rust wrote:
>
>
> On Sat, Nov 13, 2010 at 11:36 PM, Dmitry Pavlov <dp...@gg...
> <mailto: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
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