Sanitize SMARTS and Generate Coordinates for a Molecule
This workflow snippet demonstrates how to sanitize SMARTS from a drawn structure, so they can be used as query. In this case, the SMARTS is used to generate coordinates according to a drawn scaffold, to align molecules. It works fine without sanitization in some cases, but especially for structures involving aromaticity it fails. In this workflow snippet it is shown how to generate sanitized query SMARTS using two RDKit nodes. We configure the sanitization of the "drawn" SMARTS in the advanced tab of the RDKit from Molecule node. To compare the sanitized and the unsanitized SMARTS, view the output of the RDKit to Molecule node. Right-click on the column headers, and change the renderer to String. Recognize how the sanitized SMARTS allows double-bonds at any position.
The sanitized SMARTS string is then used to generate coordinates for a table of molecules. This leads to a more standardized alignment of the molecules, with the pre-defined moiety being in the same orientation in all cases.
Required extension: RDKit