A Software Package for Chemically Inspired Graph Transformation
Chemical reaction networks can be automatically generated from graph grammar descriptions, where transformation rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the transformation mu
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Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark {jlandersen,daniel}@imada.sdu.dk 2 Institute for Theoretical Chemistry, University of Vienna, 1090 Wien, Austria [email protected] 3 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany 4 Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany 5 Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany 6 Center for Non-coding RNA in Technology and Health, University of Copenhagen, 1870 Frederiksberg, Denmark [email protected] 7 Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA 8 Research Network Chemistry Meets Microbiology, University of Vienna, 1090 Wien, Austria 9 Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan [email protected]
Abstract. Chemical reaction networks can be automatically generated from graph grammar descriptions, where transformation rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the transformation must be performed on multisets of graphs. We present a general software package for this type of graph transformation system, which can be used for modelling chemical systems. The package contains a C++ library with algorithms for working with transformation rules in the Double Pushout formalism, e.g., composition of rules and a domain specific language for programming graph language generation. A Python interface makes these features easily accessible. The package also has extensive procedures for automatically visualising not only graphs and transformation rules, but also Double Pushout diagrams and graph languages in form of directed hypergraphs. The software is available as an open source package, and interactive examples can be found on the accompanying webpage. Keywords: Double Pushout · Chemical graph transformation system Graph grammar · Rule composition · Strategy framework
c Springer International Publishing Switzerland 2016 R. Echahed and M. Minas (Eds.): ICGT 2016, LNCS 9761, pp. 73–88, 2016. DOI: 10.1007/978-3-319-40530-8 5
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Introduction
It has been common practice in chemistry for more than a century to represent molecules as labelled graphs, with vertices representing atoms, and edges representing the chemical bonds between them [23]. It is natural, therefore, to formalize chemical reactions as graph transformations [6,11,13,20]. Many computational tools for graph transformation have been developed; some of them are either specific to chemistry [21] or at least provide special features for chemical systems [18]. General graph transformation tools, such as AGG [24], have also been used to modelling chemical systems [11]. Chemical graph transformation, however, differs in one crucial aspect from the usual setup in the graph transformation literature, where a single (usually connected) g
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