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.