A Software Package for Chemically Inspired Graph Transformation

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

    Publikation: Kapitel i bog/rapport/konference-proceedingKonferencebidrag i proceedingsForskningpeer review

    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.
    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
    Land/OmrådeØstrig
    ByVienna
    Periode05/07/201606/07/2016
    Internetadresse
    NavnLecture Notes in Computer Science
    Vol/bind9761
    ISSN0302-9743

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