Re: [Cdk-devel] Double Bond Configuration

[Cyrus H. <ch...@bo...>]

Ok, I'm happy enough with a broad definition of stereochemistry.

As for the local configuration issue, the point is that whether a compound is E or Z depends on priority of the substituents, whereas the UP/DOWN relationships specified by SMILES strings depends only on the (relative) configuration of the atoms attached to the atoms at the ends of the double bond. It also allows for partial specification of stereochemistry which, I would imagine, might be important for building molecules in, say, an editor where one might add constraints incrementally.

I'd like to propose some additional constants like DOUBLE_BOND_UP and and the IDoubleBondConfiguration interface, and an appropriate implementation class, that I mentioned before. Any objections/alternative suggestions?

thanks,

Cyrus


On Jul 4, 2010, at 8:41 AM, Christoph Steinbeck wrote:

> Dear Cyrus,
> 
> first of all, thanks for the initiative. I agree that it is very
> desirable to get better support for this in CDK.
> Since Egon has only recently been busy implementing the
> ITetrahedralChirality, I'm sure he will comment.
> With respect to your comment on "stereo", my personal education taught
> me something along the lines of what Wikipedia and most text books say:
> "Stereochemistry, a subdiscipline of chemistry, involves the study of
> the relative spatial arrangement of atoms within molecules. "
> 
> In that respect, we are ok.
> 
> In my group, a coworker who by now left the team had been working on
> code for the detection of double bond stereo chemistry from 2D drawings .
> This is were E_Z_BY_COORDINATES came from.
> 
> I'm not quite sure I understand that thingy with the local
> configuration. E/Z only refers to the local configuration around stereo
> bonds also.
> 
> Cheers, Chris
> 
> 
> 
> On 04/07/2010 00:00, Cyrus Harmon wrote:
>> 
>> Dear CDK Developers,
>> 
>> The IBond interface has a Stereo enum for describing stereo configurations, along with get/setStereo methods. There's also the IStereoElement interface and the ITetrahedralChirality interface. I'm interested in seeing CDK better support configurations around double bonds. In particular, I would like to be able to read and write chiral smiles specifications and I'd like for the 2D layout code to respect explicit configurations around double bonds.
>> 
>> There are a couple of ways one might go about solving this. First, there are some existing comments, E, Z, E_OR_Z, and E_Z_BY_COORDINATES. SMILES contains a notion of "local configuration" around double bonds, rather than global E/Z specifications. It would be nice if one could provide an "orientation" for atoms connected to carbons involved in double bonds. In fact, I tried this using the Stereo.UP and DOWN constants. However, the JCP rendering code draws these as wedged bonds, suggesting that this is UP or DOWN relative to the plane of the molecule, not relative to a particular double bond. Should one just use the stereo slot or is a more elaborate representation required for this? One might imagine an IDoubleBondConfiguration interface that extends iStereoElement, for instance. Also, I think the stereo name may be a bit misleading. It's true that for chiral centers one can think of them as stereo centers, but for other kinds of configurations, there not really stereocent
> er
>> s per se. Suggestions on how I might go about extending the interfaces to better support configuration around double bonds?
>> 
>> thanks,
>> 
>> Cyrus
>> 
>> 
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> 
> -- 
> Dr. Christoph Steinbeck
> Head of Chemoinformatics and Metabolism
> European Bioinformatics Institute (EBI)
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD UK
> Phone +44 1223 49 2640; Mobile +44 7826 522319
> 
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