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A Software Package for Chemically Inspired Graph Transformation

  • Jakob L. Andersen
  • Christoph Flamm
  • Daniel Merkle
  • Peter F. Stadler
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9761)

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 

Notes

Acknowledgements

This work is supported by the Danish Council for Independent Research, Natural Sciences, the COST Action CM1304 “Emergence and Evolution of Complex Chemical Systems”, and the ELSI Origins Network (EON), which is supported by a grant from the John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation.

Supplementary material

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Department of Mathematics and Computer ScienceUniversity of Southern DenmarkOdenseDenmark
  2. 2.Institute for Theoretical ChemistryUniversity of ViennaWienAustria
  3. 3.Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany
  4. 4.Max Planck Institute for Mathematics in the SciencesLeipzigGermany
  5. 5.Fraunhofer Institute for Cell Therapy and ImmunologyLeipzigGermany
  6. 6.Center for Non-coding RNA in Technology and HealthUniversity of CopenhagenFrederiksbergDenmark
  7. 7.Santa Fe InstituteSanta FeUSA
  8. 8.Research Network Chemistry Meets MicrobiologyUniversity of ViennaWienAustria
  9. 9.Earth-Life Science Institute, Tokyo Institute of TechnologyTokyoJapan

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