The Chemical Abstract's Service generic chemical (Markush) structure storage and retrieval capability. 1. Basic concepts

The concepts and strategies presented in this paper provide a new way of viewing and representing chemical structures for both specific and generic substances. Groups such as ethyl and phenyl have generic group nodes in the connection tables as alternatives to their specific atom designations. A set of 11 generic group nodes is used. The generic group nodes are hierarchical and can be further qualified by attributes such as the carbon range and ring size. Colloquial generic groups such as alkym and aryl are likewise mapped onto the hierarchical generic group nodes and appropriate attributes. The fragments of variable groups in the input representation are attached to the appropriate portion of the structure as simple alternatives at a designated point of variability. Points of variability are sometimes algorithmically shifted in the structure to simplify further processing. The resulting topological representation enables searching of specific or generic substances with structure queries consisting of all generic groups, all specific atom groups, or any combination of specific atom and generic groups, and with or without expressed variability