Biomass (Python)¶

raven-toolbox objects in raven_toolbox.biomass, collected from the source of the tracked branch.

Functions¶

Function	Summary
`BiomassComponent`	One component of the biomass equation (protein, carbohydrate, …).
`BiomassConfig`	Container for the per-organism biomass layout.
`rescale_pseudoreaction`	Multiply the substrate coefficients of one component pseudoreaction
`scale_biomass`	Rescale a component to a new mass fraction, optionally balancing
`set_gam`	Set GAM (and optionally NGAM) on a model in place.
`sum_biomass`	Mass-fraction (g/gDW) per biomass component plus the total.

Reference¶

BiomassComponent¶

One component of the biomass equation (protein, carbohydrate, …).

Attributes:

Name	Type	Description
`name`	`str`	Canonical short name — also the `model.metabolites` name of the metabolite that the pseudoreaction produces. Used by :func:`rescale_pseudoreaction` to identify the product side.
`pseudoreaction_name`	`str`	`model.reactions[*].name` of the pseudoreaction. cobrapy reactions are looked up by `name` (not `id`) because that is how the yeast-GEM convention names them.
`mass_strategy`	`MassStrategy`	How to convert the pseudoreaction's substrates into a mass fraction. See :data:`MassStrategy` for the choices and their offsets.

BiomassConfig¶

Container for the per-organism biomass layout.

Attributes:

Name	Type	Description
`biomass_rxn`	`str`	`model.reactions[*].id` of the top-level biomass pseudoreaction (the one whose flux is the growth rate).
`proton_met`	`str`	`model.metabolites[*].id` of the cytosolic H+ metabolite — used by :func:`rescale_pseudoreaction` to keep each pseudoreaction charge-balanced after rescaling.
`components`	`tuple[BiomassComponent, ...]`	Ordered tuple of :class:`BiomassComponent` describing every non-top-level pseudoreaction that contributes to mass.

get ¶

get(component_name: str) -> BiomassComponent

Look up a component by name (raises KeyError if missing).

rescale_pseudoreaction¶

Multiply the substrate coefficients of one component pseudoreaction by factor and rebalance H+ to preserve charge neutrality.

Ports rescalePseudoReaction.m. "Substrate" here means any metabolite whose name is not the component's product name; the component's own metabolite (e.g. protein for the protein pseudoreaction) is left untouched. After the rescaling the coefficient of config.proton_met is recomputed so the reaction's total ionic charge sums to zero.

scale_biomass¶

Rescale a component to a new mass fraction, optionally balancing out a second component to keep the total at 1 g/gDW.

Ports scaleBioMass.m. The rescaling factor is derived from :func:sum_biomass on the current model state, so call this with an in-place model mutation, not on a stale snapshot.

set_gam¶

Set GAM (and optionally NGAM) on a model in place.

Scales every metabolite participating in the biomass pseudoreaction whose name is in cofactor_met_names (e.g. ATP, ADP, H2O, H+, phosphate) to ±value, preserving the sign of its current coefficient.

If both ngam_rxn and ngam_value are given, the NGAM reaction's bounds are fixed at (ngam_value, ngam_value).

Parameters:

Name	Type	Description	Default
`model`	`Model`	cobra model to mutate.	required
`value`	`float`	New GAM value (mmol ATP / gDW per growth unit).	required
`biomass_rxn`	`str`	Reaction id of the biomass pseudoreaction whose stoichiometry carries the GAM coefficients.	required
`cofactor_met_names`	`Iterable[str]`	Iterable of metabolite names (not ids) — every metabolite in the biomass pseudoreaction whose name is in this set will be rescaled. yeast-GEM uses `{"ATP", "ADP", "H2O", "H+", "phosphate"}`.	required
`ngam_rxn`	`str \| None`	Optional NGAM update. If both are provided, the reaction's bounds are set to `(ngam_value, ngam_value)` (equality constraint).	`None`
`ngam_value`	`str \| None`	Optional NGAM update. If both are provided, the reaction's bounds are set to `(ngam_value, ngam_value)` (equality constraint).	`None`

Returns:

Type	Description
`Model`	The (mutated) model, for chaining.

sum_biomass¶

Mass-fraction (g/gDW) per biomass component plus the total.

Mirrors yeast-GEM's sumBioMass.m. Returns a dict keyed by each :class:BiomassComponent name plus "total". Components whose pseudoreaction is missing from the model contribute 0 (logged as a warning).

Substrate detection: in each component's pseudoreaction, the substrate side is the metabolites with negative coefficient — the same convention yeast-GEM uses.