MetabolicReactions

class cobrame.MEReaction(id=None, name='')[source]

MEReaction is a general reaction class from which all ME-Model reactions will inherit

This class contains functionality that can be used by all ME-model reactions

Parameters:id (str) – Identifier of the MEReaction. Should follow best practices of child class
add_biomass_from_subreactions(process_data, biomass=0.0)[source]

Account for the biomass of metabolites added to macromolecule (protein, complex, etc.) due to a modification such as prosthetic group addition.

Parameters:
Returns:

Initial biomass value + biomass added from subreactions in kDa

Return type:

float

add_subreactions(process_data_id, stoichiometry, scale=1.0)[source]

Function to add subreaction process data to reaction stoichiometry

Parameters:
  • process_data_id (str) –

    ID of the process data associated with the metabolic reaction.

    For example, if the modifications are being added to a complex formation reaction, the process data id would be the name of the complex.

  • stoichiometry (dict) – Dictionary of {metabolite_id: float} or {metabolite_id: float * (sympy.Symbol)}
  • scale (float) – Some processes (ie. tRNA charging) are reformulated such that other involved metabolites need scaling
Returns:

Stoichiometry dictionary with updated entries

Return type:

dict

check_me_mass_balance()[source]

Checks the mass balance of ME reaction, ignoring charge balances

Returns:{element: number_of_elemental_imbalances}
Return type:dict
clear_metabolites()[source]

Remove all metabolites from the reaction

get_components_from_ids(id_stoichiometry, default_type=<class 'cobrame.core.component.Metabolite'>, verbose=True)[source]

Function to convert stoichiometry dictionary entries from strings to cobra objects.

{metabolite_id: value} to {cobrame.core.component.Metabolite: value}

Parameters:
  • id_stoichiometry (Dict {string: float}) – Input Dict of {metabolite_id: value}
  • default_type (String) – The type of cobra.Metabolite to default to if the metabolite is not yet present in the model
  • verbose (Boolean) – If True, print metabolites added to model if not yet present in model
Returns:

{cobrame.core.component.Metabolite: float}

Return type:

dict

objective_coefficient

Get and set objective coefficient of reaction

Overrides method in parent class in order to enable use of optlang interfaces.

Returns:Objective coefficient of reaction
Return type:float
class cobrame.MetabolicReaction(id)[source]

Irreversible metabolic reaction including required enzymatic complex

This reaction class’s update function processes the information contained in the complex data for the enzyme that catalyzes this reaction as well as the stoichiometric data which contains the stoichiometry of the metabolic conversion being performed (i.e. the stoichiometry of the M-model reaction analog)

Parameters:id (str) – Identifier of the metabolic reaction. As a best practice, this ID should use the following template (FWD=forward, REV=reverse): “<StoichiometricData.id> + _ + <FWD or REV> + _ + <Complex.id>”
keff

float – The turnover rete (keff) couples enzymatic dilution to metabolic flux

reverse

boolean – If True, the reaction corresponds to the reverse direction of the reaction. This is necessary since all reversible enzymatic reactions in an ME-model are broken into two irreversible reactions