2.1.2.2. enkie.compartment_parameters

Parameters for the compartments of a biochemical network.

2.1.2.2.1. Module Contents

enkie.compartment_parameters.COMPARTMENT_ANY = '__any__'

Pseudo-identifier representing any compartment.

class enkie.compartment_parameters.CompartmentParameters(compartment_pH: Dict[str, enkie.constants.Q] = None, compartment_pMg: Dict[str, enkie.constants.Q] = None, compartment_I: Dict[str, enkie.constants.Q] = None, compartment_phi: Dict[str, enkie.constants.Q] = None, T: enkie.constants.Q = DEFAULT_T)

Parameters for the compartments of a metabolic network.

Parameters:

• compartment_pH (Dict[str, Q], optional) – Mapping from compartment identifiers to the pH of the compartment.

• compartment_pMg (Dict[str, Q], optional) – Mapping from compartment identifiers to the pMg of the compartment.

• compartment_I (Dict[str, Q], optional) – Mapping from compartment identifiers to the ionic strength of the compartment.

• compartment_phi (Dict[str, Q], optional) – Mapping from compartment identifiers to the electrostatic potential of the compartment.

• T (Q, optional) – Temperature of the system (temperature must be the same for all compartments).

pH(compartment: str) → enkie.constants.Q

Gets the pH of a compartment.

pMg(compartment: str) → enkie.constants.Q

Gets the pMg of a compartment.

I(compartment: str) → enkie.constants.Q

Gets the ionic strength of a compartment.

phi(compartment: str) → enkie.constants.Q

Gets the electrostatic potential of a compartment.

T() → enkie.constants.Q

Gets the temperature of the system.

static load(params_file: Union[pathlib.Path, str]) → CompartmentParameters

Loads the compartment parameters from a .csv file.

Parameters:

params_file (Union[Path, str]) – Path to the file containing the parameter values or name of a builtin parameter set (any file present in data/compartment_parameters/, e.g. ‘e_coli’ or ‘human’).

Returns:

New instance of this class, containing the parameters loaded from the file.

Return type:

CompartmentParameters