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The Graph Grammar Library- a generic framework for chemical graph rewrite systems

By Martin Mann, Heinz Ekker, Christoph Flamm and Convert From

Abstract

Graph rewrite systems are powerful tools to model and study complex problems in various fields of research [7]. Their successful application to chemical reaction modelling on a molecular level was shown [1, 2, 6] but no appropriate and simple system is available at the moment [8]. The Graph Grammar Library (GGL), presented in this contribution and more extensively in [4], fills this gap and provides feature-rich functionality especially for chemical transformation. The GGL implements a simple generic Double Push Out approach for general graph rewrite systems [7] on labeled undirected graphs. The object oriented C++ framework focuses on a high level of modularity as well as high performance, using state-of-the-art algorithms and data structures, and comes with extensive end user and API documentation. Central modules (e.g. graph matching, match handling, graph storage) are combined via simple interfaces, which enables an easy combining to tackle the problem at hand. The large GGL chemistry module enables extensive and detailed studies of chemical systems. It well meets the requirements and abilities envisioned by Yadav et al. [8] for such chemical rewrite systems. Here, molecules are represented as vertex and edge labeled undirected graphs while chemical reactions are described by according graph grammar rules, see Fig. 1. Such a graph grammar is a generating system for the explicit construction of an entire chemical space, O C=CC=

Topics: convert from
Year: 2014
OAI identifier: oai:CiteSeerX.psu:10.1.1.415.689
Provided by: CiteSeerX
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