ChemAxon Standardizer Remove Absolute Chemistry problem

Hi all,
I’m not sure if this is the correct place to ask this as I think this node is made by an external team, but I’m hoping others may use it.

I have an sdf containing a large number of chemical structures, some of which contain enhanced stereochemistry with Abs flags. I need to remove the Abs flag, but keep the wedged/dashed bonds as drawn.

I think the ChemAxon Standardizer node should be able to do this using the Remove Absolute Stereo option, but this doesn’t seem to work. The StandardizerResult column is detecting the structures needing changes, but the structure isn’t being changed. Am I misunderstanding what this node can do?


Your understanding of what should happen with the Standardizer node using the Remove Absolute Stereo action is correct. It should remove the Abs flag and do nothing else.
While I am not exactly sure why you observe the behavior that you do, I suspect it is because of a Java 17 incompatibility issue with the underlying code. New Chemaxon/Infocom nodes were released yesterday (version 4.4.0.v222000) and should remediate this issue. So I encourage you to try the latest nodes.
If the problem persists, it would be best to create a support ticket on the Chemaxon website.

Best regards,

Thanks for the information. I’ll have a look in my test system for updated nodes.

This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.