Language-oriented rule-based reaction network generation and analysis: Algorithms of RING

• RING has an extensible domain specific language user interface.
• Graph traversal methods used in pathway and mechanism identification features.
• New hashing based identification of functional equivalence for molecule lumping.
• Generic algorithm for group additivity based estimation of molecular properties.
• Rule-based scheme for kinetics specification for kinetic modeling.

The underlying algorithms of the language interface and post-generation analysis modules in RING, a network generation and analysis tool, are discussed. The front-end is a domain-specific reaction language developed with Silver, a meta-language based on attribute grammars. The language compiler translates user inputs written as a program into internal instructions, catches syntactic and semantic errors, and performs domain-specific optimization to speed up execution. In addition to generating reaction networks, RING allows post-processing analysis options to: (a) obtain reaction pathways and overall mechanisms from initial reactants to desired products using graph traversal algorithms, (b) group together isomers to reduce the size of the network through a novel molecule hashing technique, (c) calculate thermochemical quantities through semi-empirical methods such as group additivity, and (d) formulate and solve kinetic models of the entire or lumped complex network based on a rule-based kinetics specification scheme.