RDKit Chemical Transformation Node May Have Issues With Intermediate Products

[manuelschwarze]

Taka Ohshima [email protected] has detected an issue in his workflows related to the RDKit Chemical Transformation node, he wrote:
I am trying to convert a carboxylic acid to an amide with the following reaction smarts.
#6;A:1-! @[#8;H1:3]>>*:1-[#7:3]
However, when I process against a dicarboxylic acid, I get an error message. Also, only one of the carboxylic acids is amide-converted (not all carboxylic acids are processed; I have set Maximum Number Of Reaction Cycle = 100). Attached is a workflow to demonstrate this. QA2024_024_ChemicalTransformation.zip

The problem that @greglandrum identified was the following: The problem is being called because the chemical transformation node is not sanitizing the intermediate molecules. This means that ring information is not being re-generated and Taka's query, which uses ring features, leads to an exception. Adding sanitization will cause some intermediate products to fail, but these are almost certainly going to be removed later anyway when the final products are sanitized.

Bugfix: Instead of sanitizing only the end resulting molecule, we will do this now already for the intermediate products. This will lead to slightly different error messages when sanitization fails, but it will fix issues like the one Taka has reported.

[manuelschwarze]

Fixed in latest version 4.12 (for KNIME <5.3) and 5.2 (for KNIME 5.3+).