This talk will discuss the problems of interconverting not-entirely-compatible structure query representations. Specifically, the conversion of MDL RGfiles to SMARTS strings will be described, and issues such as R-groups, link atoms, implicit/explicit hydrogens, and aromaticity, and the compromises needed in their conversion, will be covered. In addition, the conversion of MDL RxnFiles to Reaction SMARTS and SMIRKS strings will be described, and algorithms for the automatic assignment of atom maps will be outlined.
Daylight Chemical Information Systems, Inc.