This pull request includes various enhancements to the pyology package, focusing on expanding metabolite and enzyme data, adding new reactions, and improving the energy calculation functions. The most important changes include adding categories and tags to metabolites, introducing new enzymes and reactions, and enhancing the energy calculation functions with detailed docstrings and type hints.
pyology/common_enzymes.py: Added attributes such as inhibitors, activators, active, downstream_enzymes, and hill_coefficients to enzyme definitions.
Introduction of New Reactions:
pyology/common_reactions.py: Added a new class KrebsCycleReactions with detailed definitions for each reaction in the Krebs cycle.
Improvements to Energy Calculation Functions:
pyology/energy_calculations.py: Enhanced functions with detailed docstrings and type hints, including get_quantity, calculate_base_energy_state, calculate_cell_energy_state, calculate_glycolysis_energy_state, and calculate_total_adenine_nucleotides. [1][2][3][4]
Bug Fix:
pyology/cytoplasm.py: Fixed a bug in the validate_conservation function by correcting the parameters passed to execute_command.
This pull request includes various enhancements to the
pyologypackage, focusing on expanding metabolite and enzyme data, adding new reactions, and improving the energy calculation functions. The most important changes include adding categories and tags to metabolites, introducing new enzymes and reactions, and enhancing the energy calculation functions with detailed docstrings and type hints.Enhancements to Metabolite Data:
pyology/basic_metabolites.json: Addedcategoryandtagsattributes to each metabolite entry for better classification and metadata. [1] [2] [3] [4]Enhancements to Enzyme Data:
pyology/common_enzymes.py: Added attributes such asinhibitors,activators,active,downstream_enzymes, andhill_coefficientsto enzyme definitions.Introduction of New Reactions:
pyology/common_reactions.py: Added a new classKrebsCycleReactionswith detailed definitions for each reaction in the Krebs cycle.Improvements to Energy Calculation Functions:
pyology/energy_calculations.py: Enhanced functions with detailed docstrings and type hints, includingget_quantity,calculate_base_energy_state,calculate_cell_energy_state,calculate_glycolysis_energy_state, andcalculate_total_adenine_nucleotides. [1] [2] [3] [4]Bug Fix:
pyology/cytoplasm.py: Fixed a bug in thevalidate_conservationfunction by correcting the parameters passed toexecute_command.