2. pyTFA models

pyTFA models are based on COBRApy models, with additional values.

2.1. Compartment data

This is the compartments attribute of the model. It is a dict where each key is the symbol of a compartment, and the value is another dict with the following keys :

c_min	float The minimum concentration for each metabolite in the compartment, in mol.L-1
c_max	float The maximum concentration for each metabolite in the compartment, in mol.L-1
ionicStr	float The ionic strength of the compartment (mV)
membranePot	dict A dictionnary representing the membrane potential between this compartment (which is the source compartment) and the others. Each key is the symbol of another compartment (which is the destination compartment), and the value is the potential (in mV) from the source to the destination.
name	string The name of the compartment
pH	float The pH in the compartment
symbol	string The symbol of the compartment (which is the key of this dictionnary)

Here is an example:

cobra_model.compartments['c'] = {
  'c_max': 0.01,
  'c_min': 9.9999999999999995e-08,
  'ionicStr': 0.25,
  'membranePot': {
    'c': 0,
    'e': 60,
    'g': 0,
    'm': -180,
    'n': 0,
    'p': 0,
    'r': 0,
    't': 0,
    'v': 0,
    'x': 0
  },
  'name': 'Cytosol',
  'pH': 7.0,
  'symbol': 'c'
}

2.2. Metabolites

Each metabolite must be annotated with its SeedID, which will be used to get the thermodynamic values from the Thermodynamic Databases. In order to do this, use the annotation attribute of each metabolite. Here is an example:

cobra_model.metabolites[0].annotation = {
  'SeedID': 'cpd00018'
}

pyTFA will also define a thermo a thermo attribute for each metabolite, which is a pytfa.thermo.MetaboliteThermo.

2.3. Reactions

pyTFA will define a thermo attribute for each reaction. It is a dict with the following attributes:

computed	bool Whether the thermodynamic values were computed or not.
deltaGR	float Sum of the non-concentration terms for the reaction. Used as the right-hand side value of a constraint. If the thermodynamic values were not computed, this is 10**7.
deltaGRerr	float Error on deltaGR If the thermodynamic values were not computed, this is 10**7.
deltaGrxn	float Sum of the deltaGF of all the metabolites in the reaction. Not defined if computed is False !
isTrans	bool Whether the reaction is a transport reaction or not

Here are some examples:

cobra_model.reactions[0].thermo = {
  'computed': False,
  'deltaGR': 10000000,
  'deltaGRerr': 10000000,
  'isTrans': False
}

cobra_model.reactions[99].thermo = {
  'computed': True,
  'deltaGR': 1.161097833014658,
  'deltaGRerr': 2,
  'deltaGrxn': 0,
  'isTrans': True,
}