Substructure Matcher

Community Extensions
1

Hi,

Is it possible to have a checkbox in the config box to do an Exact structure search too. This saves putting lots of explicit hydrogens everywhere in the query molecule.

Thanks,

Simon.

PS. I like the aligned matched structures, thats really handy for visualisation. And the highlighting functionality too is great.

You've done a great job on these new nodes.

2

Simon,

Such a functionality is not hard to implement, either in the Substructure Matcher node or as a new "Exact Matcher" node -- need to think about that. However, could you please describe how you see this node in action? What problem doyou want to solve with it? It is particularly interesting to know whether you have query features ("A" atoms etc.) in your query structure; do you need tautomer/resonance matching or not?

 

Best regards,

Dmitry

3

Its really for use by other chemistry users where a table of SAR information has been loaded into KNIME along with the structures,which are then converted to Indigo format. A chemist may have an exact molecule in mind they want to bring up the SAR information on. By using a chemical sketcher they would need to put explicit hydrogens everywhere to get just the result they want under the current situation. The alternative would be to convert everything to canonicalised smiles and then do a row filter which is cumbersome, I would like it very user friendly with either a tick box in the SubStructure Matcher for an Exact Match, or as you mention an "Exact Structure Matcher".

If you get it to do something as complicated as an Exact Match of tautomers/resonance matching then that would be really great. In terms of use of A atoms, I wasnt thinking of allowing that, but again if you can get an A atom to represent any atom, but not more than one heavy atom, that again would be a powerful extra feature.

So basically, I would be happy with a basic Exact Structure Matcher, but ecstatic if these extra options you mention were possible. Chemists often want to do substructure searching most of the time, and exact structure searching some of the time, so I would want it in such a way that modification of the KNIME workflow is kept to a minimum (i.e. the same node, or just swapping one node over).

Thanks

Simon.

4

Simon,

I have added the "exact" option to the Substructure Matcher node. You can check it out tomorrow morning, when the next nightly build is available. You can use query features, resonance and tautomer options with this flag.

 

Best regards,

Dmitry

5

Thanks Dmitry, this is brilliant it works exactly as expected and is really nice and user friendly for chemists to use.I think its really good having the exact match option within the substructure node as it means the workflow stays the same keeping it easy and simple.

 

Thanks so much,

Simon.

6

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