How can I use the Murcko Scaffold output as input for the R-Group Decomposer? I am looking for a way to see which positions of the Scaffolds are substituted with what.
With the current version you have to convert the output of the Murcko Scaffold Node from a query format to ordinary format: you need to use Indigo To Molecule, and Query Molecule to Indigo nodes sequentially.
I see that it is not very convenient and obvious, and we will try to implement some interface to accept arbitrary formats with automatic conversion.
I've tried the above method but the R-Group Decomposer returns an empty table. The error message is: "Error while decompose molecules: R-Group deconvolution: no embeddings obtained".
Did you succeeded in this operation?
Yes we have resolved the issue with the "R-Group deconvolution: no embeddings obtained" error. The new RGroup Decomposition API was applied for the node and from a next version the incorrect matching will only raise a warning.
The fixed version is almost prepared to be released. I will inform in this topic if the upcoming release is available.
With best regards,