2013/04/04 by Martin Mann, Mann, Martin, Heinz Ekker +3
Computer Science · Decision Sciences · #Biomolecules (q-bio.BM) #Computational Engineering #FOS: Biological sciences #FOS: Computer and information sciences #Finance #Graph Theory and Algorithms #Mathematical Software (cs.MS) #Model-Driven Software Engineering Techniques #Molecular Networks (q-bio.MN) #Scientific Computing and Data Management #and Science (cs.CE)
paper · pdf · doi:10.48550/arxiv.1304.1356
openalex publication_date 2013/04/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Graph rewrite systems are powerful tools to model and study complex problems\nin various fields of research. Their successful application to chemical\nreaction modelling on a molecular level was shown but no appropriate and simple\nsystem is available at the moment.\n The presented Graph Grammar Library (GGL) implements a generic Double Push\nOut approach for general graph rewrite systems. The framework focuses on a high\nlevel of modularity as well as high performance, using state-of-the-art\nalgorithms and data structures, and comes with extensive documentation. The\nlarge GGL chemistry module enables extensive and detailed studies of chemical\nsystems. It well meets the requirements and abilities envisioned by Yadav et\nal. (2004) for such chemical rewrite systems. Here, molecules are represented\nas undirected labeled graphs while chemical reactions are described by\naccording graph grammar rules. Beside the graph transformation, the GGL offers\nadvanced cheminformatics algorithms for instance to estimate energies\nofmolecules or aromaticity perception. These features are illustrated using a\nset of reactions from polyketide chemistry a huge class of natural compounds of\nmedical relevance.\n The graph grammar based simulation of chemical reactions offered by the GGL\nis a powerful tool for extensive cheminformatics studies on a molecular level.\nThe GGL already provides rewrite rules for all enzymes listed in the KEGG\nLIGAND database is freely available at\nhttp://www.tbi.univie.ac.at/software/GGL/.\n