Highlighted Structure Decomposer

Hi Dmitry,

If you do a substructure search and have the matched substructure highlighted in the results, would it be possible to have a node which can take this and then remove the highlighted structure to leave the remaining fragment(s) in a separate column(s) in which the fragments are left with the connecting point, like what happens with the R-Group Decomposer.

This will be a really useful node for when you get round to doing a "R Group Enumerator" node. For example you could take a series of commercially available alkyl bromides imported into KNIME, then do a substructure search on Bromine, and then run it through the "Highlighted Structure Decomposer" to give a set of R groups with a connecting point on them (where the Bromine used to be), these can then be passed into a future "R Group Enumerator" node along with a scaffold template with Rx groups around it to enumerate a set of products.



Well, you mentioned that the R-Group Decomposer does that, so why not use it? :)

You can pass the matched results (does not matter highlighted or not) to the first port of the R-Group Decomposer node, and then fork the substructure query to the second port of the node. The node will do its job and place the remaining fragments in separate columns.

Sorry if I misunderstood something. I will be happy to know the details in that case...

Best regards,


Ok you're right :-)

Attaching the results from a substructure node to the RGroup Decomposer node will do it for me, and I specify the query molecule scaffold as just as Bromine atom. Thanks for the help.

I know you were not so keen last time I mentioned it, but I still think it would be more user friendly for the RGroup Decomposer node to be able to handle structures which does not contain a part of the structure matching the scaffold. Instead of returning an error on the node, it would be better if it could just parse these molecules to a second outport unchanged, and move on to the next molecule. I do think other users are going to run in to problems with how it is setup currently.