"Either" double bond

Hi,





I'm trying to use the standardizer to change a "standard" double bond into an ISIS "either" bond (see file attached).





To do so I've tried a transformation (which doesn't work because it seems that SMILES don't support this type of bond) and a cleaning using a template (which doesn't do anything).





Could anyone help on this?


Thanks in advance.





Geoffroy.

I tried to create a transform in the standardization definition to convert cis and trans double bonds to unspecified stereo, and I failed. Houston, we have a problem. We will examine it.





But there is a handy alternative solution in Standardizer. Please use the clear stereo action instead of a transform action and check the "double bond" option. It will remove stereo info from all stereo double bonds generating an unspecified stereo representation (wiggly tail).


(The wiggly is the preferred representation of unspecified stereo double bonds by IUPAC, the crossed variation is not.)





I tested it and works fine, however, the double bond in you compound is not a stereo double bond owing to the symmetry of the molecule. So changing it to either stereo, would not make any difference in chemistry.





For whatever reason, the wiggly tailed non-stereo double bonds is not sufficient for you and still need to convert your double bonds to crossed ones, please send me here a message.

Hi,


Thanks for your quick reply.





I've tried the wiggly tail and it works fine. It's a very good suggestion.


But it seems that then the generated SDfiles are not readable in ISIS for Excel, which could be a problem.





Another potential problem could be that we are doing this for a client and, being clients, they might not like it that way.


So I'd still be interested in making "crossed" bonds...





Thanks,





Geoffroy.

Hi again,


Just to say that I've checked and as feared, our client only wants crossed bonds...





Thanks for any help on this.





Regards,





Geoffroy.

Hi,





OK, we will add a new action to Standardizer for converting the wiggly representation of "either" double bonds to crossed.


It will be available in the next release.





Best regards,


Zsolt

That's excellent!


Thanks!





Geoffroy.

Hi,





This feature is available starting with JChem version 3.2.6 .


It can be downloaded from here: http://www.chemaxon.com/jchem/download.html





Best regards,


Zsolt

It doesn't look like the wiggy to crossed conversion is working in standardiser 3.2.6





Unless I'm doing something wrong......

I might be able to help here, as I had at 1st a problem with this.


You need to apply a "remove stereochemistry" filter first and then apply the filter that change the representation.





That's how I got it to work.

Therein lies the problem. I don't want to remove all other stereochemistry, I just would like the wiggly bonds to change to the crossed representation.


I have a large number of chemicals which can have several stereochemical properties which I'm not willing to lose in order to gain the crossed form of double bonds.

Yes, you are right, something is wrong, I could reproduce the problem. We are checking the code.

Thanks for the swift check. Looking forward to a fix.

We will fix this error ASAP.





Until then:


1. If you have SMILES (or any other format that does not store coordinates) input perform a 2D clean before converting the double bonds to "crossed" representation.


2. Do not perform 2D clean after converting the double bonds to "crossed" representation.





This will work until we fix the error.





Regards,


Zsolt