How to name substructures/SMARTS?

[sumone-compbio]

Does a standardized naming convention exist for molecular substructures, similar to how IUPAC assigns systematic names for entire molecules? I have a set of SMARTS patterns and want to assign meaningful names to them for easier grouping and organization. I attempted to use PubChem's substructure search, but it only lists molecules containing the substructures, not their specific names. How should I go about naming and grouping these substructures systematically?

Thank you

[tentrillion]

Does a standardized naming convention exist for [SMARTS] molecular substructures, similar to how IUPAC assigns systematic names for entire molecules?

The short answer is "no", since you are using SMARTS. Molecular substructures for precisely defined substructures could be named as radicals, but "precisely defined" sort of implies using SMILES instead of SMARTS. E.g. a SMARTS like a will match any aromatic atom, which could be part of a benzyl group, a phenyl group, a naphthyl group, a pyridynyl group, etc.

Anything you do to name SMARTS substructures will be empirical. Possibly, depending on how you generated your SMARTS patterns and how complex they are, you might be able to assign semi-unique names to them. E.g. if you use PubChem, maybe take the name of the SMARTS pattern as the name of the lowest-numbered (CID) Pubchem compound that returns a hit. But that will not give you unique names if any of your SMARTS patterns overlap.