converting scaffold with R-groups to smiles

Hi there
I am trying to convert a scaffold from an sd file into a smiles / smart. The tricky bit for me is to keep the R-group numbering so that it appears in the final smiles / smarts.

When I read in a file with the “M RGP” line using the SD Reader then everything looks still ok. When I then use the RDKit From Molecule node and then the RDKit to Molecule node with output format set to smiles I do not have any R-group numbering in the smiles anymore.

FYI - I read the molecule into the RDKit and then checked the magic atom labels “_MolFileRLabel” and that is there so in theory RDKit seems to properly know about the information.

Any help is very much appreciated.

I don’t think I can reproduce this. When I run the attached workflow I get output SMILES that have isotope labels.[1] Is this different from what you see? What were you expecting?

R group labels.knwf (8.8 KB)

[1] Not necessarily the best way of doing this, but it’s what the RDKit has been doing for quite a while.

thanks for the workflow. Unfortunately I do not get smiles with isotopes (just the connection points) when I look in the output table. Could that be due to a version issue (our version is somewhat behind sometimes).

Yeah, this is one of those things that occasionally changes between rdkit releases, so it’s easy to imagine that it’s due to your somewhat older version.

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