I am trying to use RDKit to standardize structures and am having trouble. For example, If i have a molfile for Me2S+-O-, I want to convert it to M22S=O. I tried this for the Reaction SMARTs: [O-][S+](-*)-*>>*-S(=O)-*
The output molecule was then this R(v1)-S(=O)-R(v1) [after conversion of product to molfile). The methyls (or ethly, ...) are converted to generic R. What am I doing wrong? The RDK Product column says "Painting failed for [*]S([*]=O" but it converts ok to the molfile for R(v1)-S(=O)-R(v1) ok.
(It also looks like RDKIt does some autoconversions, e.g., PhN(=O)=O to PhN+(+O)-O- but I see that in the Molecular Sanitization section in RDKit Book.
Thanks