This pull request enhances the Enzyme class in the pyology package to support advanced enzyme kinetics and introduces new tests to ensure the correctness of these features. The most important changes include adding cooperative binding, various inhibition types, and enzyme activation, along with new methods for catalysis simulation and rate calculation.
Enhancements to Enzyme class:
pyology/enzymes.py: Added support for cooperative binding (Hill equation), multiple inhibition types (competitive, non-competitive, uncompetitive), and enzyme activation. Introduced new methods _calculate_kinetics, _calculate_inhibition_effects, and _calculate_activation_effects for detailed rate calculations. [1][2][3][4]
pyology/enzymes.py: Implemented catalyze method to simulate enzyme catalysis over a time step, handling multiple substrates and products, and regulating downstream enzymes.
Documentation improvements:
pyology/enzymes.py: Added comprehensive module-level docstring with example usage for the Enzyme class, demonstrating the new advanced features.
Testing enhancements:
tests/test_enzyme.py: Added new test cases in TestEnzymeKinetics and TestEnzymeCatalysis classes to verify the correctness of rate calculations and catalysis simulation, including scenarios with inhibitors, activators, and Hill coefficients.
This pull request enhances the
Enzymeclass in thepyologypackage to support advanced enzyme kinetics and introduces new tests to ensure the correctness of these features. The most important changes include adding cooperative binding, various inhibition types, and enzyme activation, along with new methods for catalysis simulation and rate calculation.Enhancements to
Enzymeclass:pyology/enzymes.py: Added support for cooperative binding (Hill equation), multiple inhibition types (competitive, non-competitive, uncompetitive), and enzyme activation. Introduced new methods_calculate_kinetics,_calculate_inhibition_effects, and_calculate_activation_effectsfor detailed rate calculations. [1] [2] [3] [4]pyology/enzymes.py: Implementedcatalyzemethod to simulate enzyme catalysis over a time step, handling multiple substrates and products, and regulating downstream enzymes.Documentation improvements:
pyology/enzymes.py: Added comprehensive module-level docstring with example usage for theEnzymeclass, demonstrating the new advanced features.Testing enhancements:
tests/test_enzyme.py: Added new test cases inTestEnzymeKineticsandTestEnzymeCatalysisclasses to verify the correctness of rate calculations and catalysis simulation, including scenarios with inhibitors, activators, and Hill coefficients.