Chapter open access publication

A Software Package for Chemically Inspired Graph Transformation

Springer Nature,

Volume 9761, 2016

DOI:10.1007/978-3-319-40530-8_5, Dimensions: pub.1040832317,


Andersen, Jakob L. * (1) (2)
Stadler, Peter F. (3) (4) (5) (6) (7) (8)

* Corresponding author



  1. (1) Tokyo Institute of Technology, grid.32197.3e
  2. (2) University of Southern Denmark, grid.10825.3e, SDU
  3. (3) University of Vienna, grid.10420.37
  4. (4) Fraunhofer Institute for Cell Therapy and Immunology, grid.418008.5
  5. (5) Leipzig University, grid.9647.c
  6. (6) Max Planck Institute for Mathematics in the Sciences, grid.419532.8
  7. (7) Santa Fe Institute, grid.209665.e
  8. (8) University of Copenhagen, grid.5254.6, KU


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.


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2016: Blocked

Research area: Science & Technology

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2016: Level 1

Research area: Science & Technology

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Times Cited: 12

Field Citation Ratio (FCR): 5.86

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