Matched Pairs node feedback

Thanks for the Matched Pairs nodes generated, these are a great addition to the KNIME toolkit in addition to the recently revamped Erlwood MP nodes too.

I noticed that the nodes require SMILES molecules as input according to the node dialog and description, but they seem to work perfectly fine with SDF for me too!

The addition of multiple cuts is a great addition which has been an unmet need. I have only had a quick play with it so far.

One addition I would like is an option to have the Matched Pairs calculated in both directions, i.e. so you can find a transformation in any direction. A chemist doesnt always want to do a substructure search on the L and R fragments both ways around, i.e. doing the search twice, as its a little cumbersome.

I think an extra node to make it more useful to MedChemists to compliment these, that would be highly desirable, is to be able to generate a similar output as achieved with the Erlwood nodes without the need for some quite complicated manipulations. What would be needed is a node which takes the MP output table and the original SAR table as inputs, and then you can specify which SAR columns you want to calculate ratios or differences on. Trying to do this on changing columns in an automated way is possible but not easy for novice users.


Thanks Simon.

Well done for spotting the deliberate mistake in the dialog and description - yes, the node should accept SMILES, sdf, mol, RDKit formats without issue.

I will add the 'both ways round' to the to do list, and have a think about the extra node request... in 2015!  Need to take a look at the new Erl Wood nodes too - they got a mention at the SIG meeting in September and sounded exciting and complimentary to ours.



The reference to SMILES in the node dialogs has now been removed, and this is release in v 1.3.1

'Both ways round' - I've looked at the source code, and I think this is do-able - more soon-ish, hopefully.

The new node request - that is, I guess, a bit 'Joiner'-like - it's going to take some more serious development work, but will put it on our list, as it does sound like a useful idea.



Just to update you - we upgraded to v 1.3.4 this afternoon, which has the option for the reverse transform, amongst other refinements.