This pull request includes several changes to the pyology package, focusing on improving logging, adjusting metabolite quantities, and refining enzyme and reaction definitions. The most important changes include modifying the logging level, updating metabolite quantities, and pausing mitochondrial ATP production.
Logging Improvements:
fun.py: Changed the logging level to DEBUG to capture all log messages.
This pull request includes several changes to the
pyologypackage, focusing on improving logging, adjusting metabolite quantities, and refining enzyme and reaction definitions. The most important changes include modifying the logging level, updating metabolite quantities, and pausing mitochondrial ATP production.Logging Improvements:
fun.py: Changed the logging level toDEBUGto capture all log messages.Metabolite Adjustments:
pyology/basic_metabolites.json: Updated initial and maximum quantities for various metabolites, including ATP, ADP, and glucose. [1] [2]Enzyme and Reaction Refinements:
pyology/common_enzymes.py: Corrected the substrate forenolaseand added a new enzymephosphoglycerate_mutase. [1] [2]pyology/common_reactions.py: Updated reaction definitions to use the correct substrates, products, and enzymes.Simulation Enhancements:
pyology/cell.py: Added methods to initialize and check adenine nucleotide balance, and paused mitochondrial ATP production. [1] [2] [3]Exception Handling:
pyology/exceptions.py: Refactored exception classes to provide more specific error handling for metabolites and reactions.These changes aim to enhance the accuracy and traceability of the simulation process, ensuring better error handling and more detailed logging.