Standardizing Queries?

User 9d765be2f7

03-04-2008 00:28:05

We have (through probably irrecoverable historical accident) a large number of nitro groups in our structure library, with large populations drawn using both the charged and uncharged forms ([O-]-[N+]=O and O=N=O). If I'm drawing a query structure into MarvinSketch, I can of course draw it using the "single or double bond", and catch all of them, but this led me to wonder: is there a way (using Standardizer or some other widget) to apply a rule-based transformation to a structure with query features? Specifically, to transform either of the above forms of a nitro group to the compromise query that will hit either one? My feeling is that reaction SMARTS won't do this, and I haven't found any indication that Standardizer should be able to, but I'm hoping I might have missed something.

ChemAxon d76e6e95eb

03-04-2008 07:04:44

Are you using JChem Base or JChem Cartridge in the database? In that case, a Standardizer configuration can be assigned to your table and your queries will work correctly either representation you use. Just append this transform to the Standardization configuration (the opposite direction will do as well):


[O-:2]-[N+:1]=O>>[O:2]=[N:1]=O





Your original molecules will remain intact, but if you insert molecules into this table, a standardized version will be generated as well. If you run a query, the query is standardized too, so your nitros will all be found, and you can display the original drawing, either the neutral or the ionic mesomer.