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A software package for chemically inspired graph transformation

: Andersen, Jakob L.; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.


Echahed, R.:
Graph transformation. 9th international conference, ICGT 2016 : In memory of Hartmut Ehrig, held as part of STAF 2016, Vienna, Austria, July 5-6, 2016; Proceedings
Cham: Springer International Publishing, 2016 (Lecture Notes in Computer Science 9761)
ISBN: 978-3-319-40529-2 (Print)
ISBN: 978-3-319-40530-8 (Online)
International Conference on Graph Transformation (ICGT) <9, 2016, Vienna>
Conference "Software Technologies - Application and Foundations" (STAF) <2016, Vienna>
Conference Paper
Fraunhofer IZI ()
chemical graph transformation system; double pushout approach; graph grammar; rule composition; strategy framework

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