title: Efficient enumeration of monocyclic chemical graphs with given path frequencies.
abstract: BACKGROUND
  The enumeration of chemical graphs (molecular graphs) satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics because it leads to a variety of useful applications including structure determination and development of novel chemical compounds.
  
  
  RESULTS
  We consider the problem of enumerating chemical graphs with monocyclic structure (a graph structure that contains exactly one cycle) from a given set of feature vectors, where a feature vector represents the frequency of the prescribed paths in a chemical compound to be constructed and the set is specified by a pair of upper and lower feature vectors. To enumerate all tree-like (acyclic) chemical graphs from a given set of feature vectors, Shimizu et al. and Suzuki et al. proposed efficient branch-and-bound algorithms based on a fast tree enumeration algorithm. In this study, we devise a novel method for extending these algorithms to enumeration of chemical graphs with monocyclic structure by designing a fast algorithm for testing uniqueness. The results of computational experiments reveal that the computational efficiency of the new algorithm is as good as those for enumeration of tree-like chemical compounds.
  
  
  CONCLUSIONS
  We succeed in expanding the class of chemical graphs that are able to be enumerated efficiently.
authors: Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University Yoshida, 606-8501 Kyoto, Japan.
authors: Masaki
authors: M
authors: Suzuki
authors: Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University Yoshida, 606-8501 Kyoto, Japan.
authors: Hiroshi
authors: H
authors: Nagamochi
authors: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011 Kyoto, Japan.
authors: Tatsuya
authors: T
authors: Akutsu
keywords: Chemical graphs; Enumeration; Feature vector; Monocyclic structure