Process thermodynamic data¶
This module implements functions that import and process thermodynamic data for plotting.
- calculate_dG(data_dict: dict, gas_constant: float, temperature: float, rxn_order: Optional[list] = None) DataFrame¶
Given a dictionary representing a GRASP input file, calculates the minimum and maximum reaction dGs based on the standard dGs in thermoRxns and metabolite concentrations in thermoMets.
- Parameters
data_dict – a dictionary that represents the excel file with the GRASP model.
gas_constant – the gas constant to calculate the Gibbs energy.
temperature – the temperature to calculate the Gibbs energy.
rxn_order – a list with the reactions order (optional).
- Returns
Gibbs energies dataframe.
- get_fluxes_and_dGs(data_dict: dict) tuple¶
Given a dictionary representing a GRASP input file, it calculates the reaction dG and possibly the reaction fluxes. It works both when all fluxes are specified in measRates and when robust fluxes are calculated for a fully determined system. If the fluxes are not fully specified or the system is not fully determined, it doesn’t work.
- Parameters
data_dict – a dictionary representing a GRASP input file.
- Returns
The fluxes and Gibbs energies dataframes.
- get_robust_fluxes(data_dict: dict, rxn_order: Optional[list] = None) DataFrame¶
Given a dictionary representing a GRASP input file, it calculates the robust fluxes (almost) as in GRASP, unless the system is not fully determined.
- Parameters
data_dict – path to the GRASP input file
rxn_order – a list with the reactions order (optional)
- Returns
fluxes_df – dataframe with flux mean and std values