A Software Package for Chemically Inspired Graph Transformation

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

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Abstrakt

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.
OriginalsprogEngelsk
TitelGraph Transformation : Proceedings of the 9th International Conference on Graph Transformation
RedaktørerRachid Echahed, Mark Minas
ForlagSpringer
Publikationsdato2016
Sider73-88
ISBN (Trykt)978-3-319-40529-2
ISBN (Elektronisk)978-3-319-40530-8
DOI
StatusUdgivet - 2016
Begivenhed9th International Conference on Graph Transformation - Vienna, Østrig
Varighed: 5. jul. 20166. jul. 2016
Konferencens nummer: 9
https://sites.google.com/site/icgt2016/

Konference

Konference9th International Conference on Graph Transformation
Nummer9
LandØstrig
ByVienna
Periode05/07/201606/07/2016
Internetadresse
NavnLecture Notes in Computer Science
Vol/bind9761
ISSN0302-9743

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Citationsformater

Andersen, J. L., Flamm, C., Merkle, D., & Stadler, P. F. (2016). A Software Package for Chemically Inspired Graph Transformation. I R. Echahed, & M. Minas (red.), Graph Transformation: Proceedings of the 9th International Conference on Graph Transformation (s. 73-88). Springer. Lecture Notes in Computer Science, Bind. 9761 https://doi.org/10.1007/978-3-319-40530-8_5