Abstract
This paper reports a comparative evaluation of four algorithms that can be used to determine the presence or absence of a set of atoms and associated interatomic distances in 3D chemical structures. The geometric searching algorithms tested are that described by Lesk for the identification of patterns in proteins, one derived from the set reduction techniques used for substructure searching in files of 2D chemical structures, a procedure based on clique detection, and Ullman's subgraph isomorphism algorithm. Tests with structures from the Cambridge Crystallographic Data Bank demonstrate the general superiority of Ullman's algorithm for data of this sort.
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