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 must be performed on multisets of graphs. We pr...

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Bibliographic Details
Published inGraph Transformation pp. 73 - 88
Main Authors Andersen, Jakob L., Flamm, Christoph, Merkle, Daniel, Stadler, Peter F.
Format Book Chapter
LanguageEnglish
Published Cham Springer International Publishing
SeriesLecture Notes in Computer Science
Subjects
Chemical graph transformation system
Double Pushout
Graph grammar
Rule composition
Strategy framework
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Summary: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.
ISBN:9783319405292
3319405292
ISSN:0302-9743
1611-3349
DOI:10.1007/978-3-319-40530-8_5