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Graph Rewriting Based Search for Molecular Structures: Definitions, Algorithms, Hardness

  • Ernst Althaus
  • Andreas Hildebrandt
  • Domenico MoscaEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10748)

Abstract

We define a graph rewriting system that is easily understandable by humans, but rich enough to allow very general queries to molecule databases. It is based on the substitution of a single node in a node- and edge-labeled graph by an arbitrary graph, explicitly assigning new endpoints to the edges incident to the replaced node. For these graph rewriting systems, we are interested in the subgraph-matching problem. We show that the problem is NP-complete, even on graphs that are stars. As a positive result, we give an algorithm which is polynomial if both rules and query graph have bounded degree and bounded cut size. We demonstrate that molecular graphs of practically relevant molecules in drug discovery conform with this property. The algorithm is not a fixed-parameter algorithm. Indeed, we show that the problem is W[1]-hard on trees with the degree as the parameter.

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Copyright information

© Springer International Publishing AG 2018

Authors and Affiliations

  • Ernst Althaus
    • 1
  • Andreas Hildebrandt
    • 1
  • Domenico Mosca
    • 1
    Email author
  1. 1.Johannes Gutenberg-Universität MainzMainzGermany

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