This pull request includes significant changes to the pyology module, focusing on metabolite data, enzyme definitions, and reaction processes. The most important changes include updating the glucose amounts in the simulation, adding a comprehensive list of metabolites, refactoring the Cell class to use a unified metabolite dictionary, and defining common enzymes and reactions for glycolysis.
Simulation and Data Updates:
fun.py: Updated glucose_amounts to a single value of [4] for simulations.
pyology/cell.py: Refactored the Cell class to use a unified metabolites dictionary instead of separate cytoplasm and mitochondrion metabolite dictionaries. This affects several methods including produce_atp, produce_atp_generator, and get_cell_state. [1][2][3][4][5][6][7]
Enzyme and Reaction Definitions:
pyology/common_enzymes.py: Added definitions for common enzymes involved in glycolysis, including Hexokinase, Phosphoglucose Isomerase, and others.
pyology/common_reactions.py: Defined common reactions for glycolysis, linking them with their respective enzymes and substrates/products.
This pull request includes significant changes to the
pyologymodule, focusing on metabolite data, enzyme definitions, and reaction processes. The most important changes include updating the glucose amounts in the simulation, adding a comprehensive list of metabolites, refactoring theCellclass to use a unified metabolite dictionary, and defining common enzymes and reactions for glycolysis.Simulation and Data Updates:
fun.py: Updatedglucose_amountsto a single value of[4]for simulations.pyology/basic_metabolites.json: Added a detailed list of metabolites with their quantities, types, and units.Refactoring and Class Improvements:
pyology/cell.py: Refactored theCellclass to use a unifiedmetabolitesdictionary instead of separate cytoplasm and mitochondrion metabolite dictionaries. This affects several methods includingproduce_atp,produce_atp_generator, andget_cell_state. [1] [2] [3] [4] [5] [6] [7]Enzyme and Reaction Definitions:
pyology/common_enzymes.py: Added definitions for common enzymes involved in glycolysis, includingHexokinase,Phosphoglucose Isomerase, and others.pyology/common_reactions.py: Defined common reactions for glycolysis, linking them with their respective enzymes and substrates/products.