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 arXiv:1603.02481v2 [cs.FL] 21 Apr 2016 is available as an open source package, and interactive examples can be found on the accompanying webpage.

Undirected labeled graphs and graph rewriting are natural models of chemical compounds and chemical reactions. This provides a basis for exploring spaces of molecules and computing reaction networks implicitly defined by graph grammars. Molecule graphs are connected, meaning that rewriting steps in general are many-to-many graph transformations. Chemical grammars are typically subject to combinatorial explosion, however, making it often infeasible to compute the underlying network by direct breadth-first expansion.To alleviate this problem, we introduce here partial applications of rules as a basis for the efficient implementation of strategies that are not only well suited for exploration of chemistries defined by graph grammars, but that are also applicable in a general graph rewriting context as well. As showcases, we explore a complex chemistry based on the Diels-Alder reaction to explore specific subspaces of the molecular space. As a non-chemical application we use the framework of exploration strategies to model an abstract graph rewriting problem to construct high-level transformations that cannot be directly represented the Double-Pushout formalism starting from simple DPO transformation rules.