tools to check if a drawn structure is correct

I'm looking for a tool like cheshire (MDL) allowing to validate that a structure is well represented (see the exemple in attached file (exemple CN.skc) where a either bond is drawn in place of a double either bond) (or an other in the 2nd attached file testCN.skc where a flag chiral is added whereas the structure is not chiral

Standardizer is a flexible tool having various actions to batch canonicalize/beautify/modify your molecules. For example, you can remove or set the chiral flag. It will certainly not set the chiral flag for a non-stereo compound.





You can download a fee evaluation version from our web page. If you realize, that a useful action is missing, just write me here.





A comment: skc is a proprietary file format of MDL, but ChemAxon tools support many other published file formats from them including mol, sdf, rxn, rdf (both V2000 and V3000 versions). Can you convert your skc files to one the above ones?

Ok I send a mol of the file testCN.skc and a jpeg of the file exempleCN.JPG.


I already saw that your tool "standardizer" can remove or set a chiral flag but


I have a sdfile (with many structures) and I would like to check if they are chiral, they are well drawn without error. Is it possible with your tool "standardizer"

I try your tool "standardizer" (windows) and it can not detect the error of the "either" bond or remove the chiral flag if a structure is not chiral (I choose the option absolute stereo)

ChemAxon supports both the crossed and the wavy representations of the double bonds, seems that the conversion is possible from the API only at the moment, not from the Standardizer application. We will either add a new action for that or enhance the Transform action to handle it.





Please note, that the latest IUPAC recommendations favour the vawy (wiggly) representation and not the crossed double bond.

and the problem of removing chiral flag if a structure is not chiral?


I try with "standardizer" and it cannor remove the flag chiral whereas the structure is not chiral (see testCN.mol)

You can remove the chiral flag first and set it after. This is applicable only of non-of your stereo molecules are racemic, though it is unlikely. We will add an option to the remove method to remove chiral flag from non-stereo molecules only.





Both of your requests are on our internal bug and feature tracking system. Thanks for the ideas!

Did you try my proposal?





- first remove the absolute stereo flag (chiral flag)


- then set absolute stereo flag (for stereo molecules only)





Did this two step standardization solve your problem?

No the 2 steps don't solve my problem.


But after check the structure is chiral (no symmetric).


I have always the problem with the "double either" bond

Hi,





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


We will also add an option to the remove method to remove chiral flag from non-stereo molecules only.





It will be available in the next release.





Best regards,


Zsolt

Quote:

We will add a new action to Standardizer for converting the wiggly representation of "either" double bonds to crossed. We will also add an option to the remove method to remove chiral flag from non-stereo molecules only. It will be available in the next release.

These features are available starting with JChem version 3.2.6 .


"Set" action of AbsoluteStereo task from now on clears the absolute stereo flag if the molecule doesn't contain chiral atom(s).





JChem 3.2.6 can be downloaded from here: http://www.chemaxon.com/jchem/download.html