RDKit not stripping salts if molecule becomes empty


I am trying to use your salt stripper and have noticed that if the molecule is made up of, say, 2 components, both of which can be considered a 'salt' in their own right, only one of the salts will be stripped. It won't strip the molecule until it's empty, which is what I want.

Is this intentional?

Pipeline pilot does this rather nicely and you can filter out the empty molecules.




Does anyone have an answer to this?


The current implementation in the RDKit Salt Stripper node is doing this by intention. It is keeping the last fragment in the molecule when stripping salts, even if it is a salt itself. 

I am putting a new feature request on our todo list to have an option that would allow you to strip down a molecule even to zero atoms. It should probably result into an empty cell (instead of an empty molecule), which would be easy to be filtered out afterwards using KNIME's Row Filter node. We will discuss details internally.


Thanks. Empty cells would be useful and easy to filter, as you said.