PAMValidator Objects

class PAMValidator(object)

MW_GLC

g/mol

GRADIENT_MAX

mmol/gdw/h

GRADIENT_STEP

mmol/gdw/h

GRADIENT_MIN

mmol/gdw/h

run_simulations_glc_o2_gradient

def run_simulations_glc_o2_gradient(
        oxygen_gradient: list,
        params_to_save: Union[str, list] = "R_TranslationalProteinSector")

Function to run simulations of different oxygen gradients for a range of growth rates.

This will simulate growth for the entire range of glucose concentrations for each oxygen uptake rate as given by the input.

Arguments:

oxygen_gradient list - List of upper bounds for the oxygen uptake reaction to loop over.
params_to_save optional - string or list, which parameter(s) to save for further analysis (default: translational protein sector constraint).

Returns:

results list of dataframes - Saves the growth rate, glucose uptake rate, and the user-defined parameters for each oxygen uptake rate in separate dataframes.

run_simulations_ups

def run_simulations_ups(
        ups_gradient: list,
        params_to_save: Union[str, list] = "R_TranslationalProteinSector")

Function to run simulations with increasing unused enzyme sectors proportions for a range of growth rates.

This will simulate growth for the entire range of glucose concentrations for a range of fractions of ups_0 as given by the input.

Arguments:

ups_gradient list - List of upper bounds for the oxygen uptake reaction to loop over.
params_to_save optional - string or list, which parameter(s) to save for further analysis (default: translational protein sector constraint).

Returns:

results list of dataframes - Saves the growth rate, glucose uptake rate, and the user-defined parameters for each oxygen uptake rate in separate dataframes.

custom_plot

def custom_plot(rxn_ids: list,
                valid_dataframe: pd.DataFrame = None,
                xaxis: str = None,
                c_uptake_rxn: str = GLUCOSE_EXCHANGE_RXNID)

Function to plot the results of custom reactions.

Arguments:

rxn_ids list of str - Reaction identifiers of the reactions to be plotted.
valid_dataframe pandas.DataFrame, optional - A DataFrame with experimental data to validate the results with. The columns should be the same as the rxn_id of the reaction to be plotted and the reaction which should be plotted on the x-axis (by default the glucose exchange reaction EX_glc__D_e_b). If the DataFrame is not provided, only the simulation results will be plotted.
xaxis str, optional - The reaction identifier of the reaction which should be plotted on the x-axis (default: EX_glc__D_e_b).

Returns:

Prints scatter plots of the model simulations vs. experimental data points (if provided).