PyEED is collaborative project on developing a sustainable, re-usable toolbox for enzyme engineering. The toolbox includes methods to establish databases on sequence, structure, and function of protein families, bioinformatics methods for analyzing sequence and structure data, modelling tools for studying substrate binding sites and for designing mutants, and data management tools for handling experimental data on enzyme function.

Have a look at the PyEED datamodel. This data model roots the base for transforming bioinfarmatical workflows from file-centered to datamodel-centered. Alternatively, check out the corresponding UML diagram

Check out the example notebooks, demonstrating the usage of th pyEED library.