A software package for chemically inspired graph transformation

DOI10.1007/978-3-319-40530-8_5MaRDI QIDQ3187804zbMATH OpenOpenAlexWikidataFDO

Authors Jakob L. Andersen, C. Flamm, Daniel Merkle, Peter F. Stadler

Publication date 5 September 2016

Published in Graph Transformation (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1603.02481

zbMATH Keywords

graph grammardouble pushoutchemical graph transformation systemrule compositionstrategy framework

Mathematics Subject Classification ID

Formal languages and automata (68Q45) Grammars and rewriting systems (68Q42) Classical flows, reactions, etc. in chemistry (92E20)

Abstract: Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the rewriting must be performed on multisets of graphs. We present a general software package for this type of graph rewriting 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 rewrite 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.

Recommendations

• Rule composition in graph transformation models of chemical reactions
• Automatic inference of graph transformation rules using the cyclic nature of chemical reactions
• Graph Transformations
• From chemical rules to term rewriting
• scientific article; zbMATH DE number 867636

Cites work

• 50 Shades of Rule Composition
• An open graph visualization system and its applications to software engineering
• Graph Transformations
• Graph Transformations
• Graph multiset transformation: a new framework for massively parallel computation inspired by DNA computing
• How to delete categorically -- two pushout complement constructions
• LATIN 2012: Theoretical informatics. 10th Latin American symposium, Arequipa, Peru, April 16--20, 2012. Proceedings
• Molecular Analysis of Metabolic Pathway with Graph Transformation
• Navigating the chemical space of HCN polymerization and hydrolysis: guiding graph grammars by mass spectrometry data

Cited in

(14)

• Context-sensitive fusion grammars and fusion grammars with forbidden context are universal
• Fundamentals of compositional rewriting theory
• Verifying polymer reaction networks using bisimulation
• scientific article; zbMATH DE number 7453970 (Why is no real title available?)
• Automatic inference of graph transformation rules using the cyclic nature of chemical reactions
• Rule composition in graph transformation models of chemical reactions
• scientific article; zbMATH DE number 7456054 (Why is no real title available?)
• Rewriting theory for the life sciences: a unifying theory of CTMC semantics
• Rewriting theory for the life sciences: a unifying theory of CTMC semantics
• Polyhedral geometry and combinatorics of an autocatalytic ecosystem
• Mathematical analysis for a class of stochastic copolymerization processes
• scientific article; zbMATH DE number 7410923 (Why is no real title available?)
• scientific article; zbMATH DE number 7456060 (Why is no real title available?)
• Graph Transformations

Describes a project that uses

Uses Software

• pgf
• GGL
• Open Babel
• Python
• BGL
• MedOlDatschgerl
• TikZ
• Boost
• PORGY
• AGG

This page was built for publication: A software package for chemically inspired graph transformation

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q3187804)