test_thermodynamics

Perform tests using eQuilibrator API on an instance of cobra.Model.

Module Contents

test_thermodynamics.test_find_candidate_irreversible_reactions(model)[source]

Identify reversible reactions that could be irreversible.

If a reaction is neither a transport reaction, a biomass reaction nor a boundary reaction, it is counted as a purely metabolic reaction. This test checks if the reversibility attribute of each reaction agrees with a thermodynamics-based calculation of reversibility.

Implementation: To determine reversibility we calculate the reversibility index ln_gamma (natural logarithm of gamma) of each reaction using the eQuilibrator API. We consider reactions, whose reactants’ concentrations would need to change by more than three orders of magnitude for the reaction flux to reverse direction, to be likely candidates of irreversible reactions. This assume default concentrations around 100 μM (~3 μM—3 mM) at pH = 7, I = 0.1 M and T = 298 K. The corresponding reversibility index is approximately 7. For further information on the thermodynamic and implementation details please refer to https://doi.org/10.1093/bioinformatics/bts317 and https://pypi.org/project/equilibrator-api/.

Please note that currently eQuilibrator can only determine the reversibility index for chemically and redox balanced reactions whose metabolites can be mapped to KEGG compound identifiers (e.g. C00001). In addition to not being mappable to KEGG or the reaction not being balanced, there is a possibility that the metabolite cannot be broken down into chemical groups which is essential for the calculation of Gibbs energy using group contributions. This test collects each erroneous reaction and returns them as a tuple containing each list in the following order:

  1. Reactions with reversibility index
  2. Reactions with incomplete mapping to KEGG
  3. Reactions with metabolites that are problematic during calculation
  4. Chemically or redox unbalanced Reactions (after mapping to KEGG)

This test simply reports the number of reversible reactions that, according to the reversibility index, are likely to be irreversible.