converting scaffold with R-groups to smiles

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1

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.
Thx

2

Hi,
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)

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

3

Hi
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).
Thx
Nik

4

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.
-greg

5

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