PyEnzyme is a comprehensive software solution for manipulating EnzymeML files. Furthermore, the library incorporates convenient access to prominent modeling platforms, such as COPASI and PySCeS, enabling a smooth progression from laboratory experiments to kinetic characterization. Additionally, PyEnzyme empowers users to generate aesthetically appealing, publication-quality visualizations, as well as export data to widely utilized formats, such as CSV and JSON.
The API uses the SBML syntax and naming conventions which are familiar to enzymologists to be implemented into EnzymeML. The basic concept of the two libraries is the usage of multiple dictionaries, in which proteins, reactants, units, and reactions are stored. They are indexed by internal IDs to prevent duplicates and ensure that they can always be traced back from reactions and vice versa. This allows an application to load multiple EnzymeML documents and filter them by user-defined properties, such as all reactions in which a certain reactant participates.
All functions were optimized to require no further knowledge of Python, such that users only have to adapt to the EnzymeML syntax.