RDkit Smiles Header


Many thanks for the implementation of the RDKit Smiles Header node this now allows the Structures to appear in the column header when the data originated outside of an RDkit node. This is Great.! I am now using this inconjunction with the Pivot node and R Group Decomp nodes.

I have got this working well, but I cannot understand what this node does when the optional inport is not used. I was assuming this was incase the table headers where already smiles strings and were just wanted to be parsed as structures into the table headers for use with RDKit Table Viewer, but this doesnt seem to be the case.

Is there an easy way to parse the column header smiles strings into structures without having to generate a second table for this instance?

Also, I am unclear what the "complete reset" option is actually doing, I see no change in the output whether this is ON or OFF.

One final minor point is the node description is a bit confusing for new users. I only understood it since there had been some requests for this feature.

Hope the feedback helps!


Hi Simon,

thanks for your valuable feedback!

When the optional second in-port is empty, the node just retrieves the SMILES that are currently set as additional header information (if there is any, e.g. as result from the RDKit substructure counter node or as result of setting them with the new RDKit SMILES Header node). To be clear: This is not the header title I am talking about. This may be something totally different. The SMILES are internally stores as a special column property, which is then used when the table headers are rendered.

The idea of using existing table header titles that are actually SMILES strings is good. I did not think of that, probably because I thought we are the only ones with the RDKit Substructure Counter that actually produce such columns (and I even improved that node so the SMILES do not have to end up as column headers). I added your idea to our improvement list -  we could have an additional option "Use column titles as SMILES input" in the RDKit SMILES Headers.

The complete reset option removes all SMILES header information (again: not the title but the property) before applying new information. So, if the optional second in-port is not connected (no input) it would remove all SMILES information without applying any new one. Subsequent views will not show any structures anymore in the column headers.

I will try to improve the node description.


Thanks Manuel for the comments.

I now understand what you mean!

I appreciate it is not easy to explain the workings of this node!



Hi Simon,

It took some time, but I hope the node is now easier to understand. And it does also what you asked for: There is an option now to use as SMILES properties the column titles, if they are SMILES values already. Please check it out from the latest nightly build and let me know what you think. Thanks!

Kind regards,




Now thats brilliant! The node description is much more clear now. Any new user should be able to determine the function of the node.

But what is really brilliant is the conversion of SMILES column names straight into Structures, absolutely amazing. This is so so useful, thanks for your time in doing this!!!

I can now just Pivot a Free Wilson table, remove extra characters from the Column Names with Rename RegEx to leave just the exact Smiles, and then use the RDKit Smiles Header now, and I now have the amazing structures as headers.




Glad, you like it :-) - See you in Zurich.