memote.support.biomass

Supporting functions for biomass consistency checks.

Module Contents

Functions

sum_biomass_weight(reaction)	Compute the sum of all reaction compounds.
find_biomass_precursors(model, reaction)	Return a list of all biomass precursors excluding ATP and H2O.
find_blocked_biomass_precursors(reaction, model)	Return a list of all biomass precursors that cannot be produced.

memote.support.biomass.sum_biomass_weight(reaction)

Compute the sum of all reaction compounds.

This function expects all metabolites of the biomass reaction to have formula information assigned.

Parameters:

reaction : cobra.core.reaction.Reaction

The biomass reaction of the model under investigation.

Returns:

float

The molecular weight of the biomass reaction in units of g/mmol.

memote.support.biomass.find_biomass_precursors(model, reaction)

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.

model : cobra.Model

The metabolic model under investigation.

Returns:

list

Metabolite objects that are reactants of the biomass reaction excluding ATP and H2O.

memote.support.biomass.find_blocked_biomass_precursors(reaction, model)

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.

Returns:

list

Metabolite objects that are reactants of the biomass reaction excluding ATP and H2O that cannot be produced by flux balance analysis.