JavaGrins with SMARTS Ragu Bharadwaj Daylight CIS Inc.

SMARTS does not allow constructs for variable numbers of an atom or group

UNIX regular expressions vs. SMARTS In UNIX regular expressions "xyxx*z" would match "xyxxx....z" No way to make the analogous query in SMARTS to match all molecules with

 
 

A nitro group Nitrogen has the  SMARTS [$([NX3](=O)=O)]. While this is trivial, creating such template SMARTS on the fly  is not error-free. Inserting this  SMARTS in a steroid can  yield a SMARTS like: OC1C([$([NX3](=O)=O)]) CC2(C3C(CCC2C1)C4CCC(C4 (CC3)C)=O)C

Sadly SMARTS is tough to use practically without a computer, since chemical queries can translate to very complex boolean operations and therefore very long SMARTS. Since we think in terms of chemical groups rather than their boolean definitions, this problem is further exacerbated without graphical tools.  However despite these limitations SMARTS provides a powerful mechanism to construct complex queries. In the past we have received several requests to produce a more chemically intuitive interface for SMARTS