memote.support.biomass module

Supporting functions for biomass consistency checks.

memote.support.biomass.sum_biomass_weight(reaction)[source]

Compute the sum of all reaction compounds.

Parameters:

reaction : cobra.core.reaction.Reaction

The biomass reaction of the model under investigation.

memote.support.biomass.find_biomass_precursors(reaction)[source]

Return a list of all biomass precursors excluding ATP and H2O.

Parameters:

reaction : cobra.core.reaction.Reaction

The biomass reaction of the model under investigation.

memote.support.biomass.find_blocked_biomass_precursors(reaction, model)[source]

Return a list of all biomass precursors that cannot be produced.

Parameters:

reaction : cobra.core.reaction.Reaction

The biomass reaction of the model under investigation.

model : cobra.Model

The metabolic model under investigation.