Authors:
Fei He
;
Akiyoshi Hanai
;
Hiroshi Nagamochi
and
Tatsuya Akutsu
Affiliation:
Kyoto University, Japan
Keyword(s):
Isomers Enumeration, Naphthalene, Chemical Graph.
Related
Ontology
Subjects/Areas/Topics:
Algorithms and Software Tools
;
Bioinformatics
;
Biomedical Engineering
;
Immuno- and Chemo-Informatics
Abstract:
In this paper, we consider the problem of enumerating naphthalene isomers, where enumeration of isomers is important for drug design. A chemical graph G with no other cycles than naphthalene rings is called tree-like, and becomes a tree T possibly with multiple edges if we contract each naphthalene ring into a single virtual atom of valence 8. We call tree T the tree representation of G. There may be more than one tree-like chemical graphs whose tree representations equal to T, which are called naphthalene isomers of T. We present an efficient algorithm that enumerates all naphthalene isomers of a given tree representation. Our algorithm first counts the number of all the naphthalene isomers using dynamic programming, and then for each k, generates the k-th isomer by backtracking the counting computation. In computational experiment, we compare our method with MolGen, a state-of-the-art enumeration tool, and it is observed that our program enumerates the same number of naphthalene is
omers within extremely shorter time, which proves that our algorithm is effectively built.
(More)