constrain: Function for constraining the models based on metabolite...

In euba/BacArena: Modeling Framework for Cellular Communities in their Environments

Function for constraining the models based on metabolite concentrations

Description

The generic function constrain changes the constraints of the model representation of an organism.

Usage

constrain(object, reacts, lb, dryweight, tstep, scale, j, cutoff = 1e-06)

## S4 method for signature 'Organism'
constrain(object, reacts, lb, dryweight, tstep, scale, j, cutoff = 1e-06)

Arguments

object	An object of class Organisms.
reacts	A character vector giving the names of reactions which should be constrained.
lb	A numeric vector giving the constraint values of lower bounds (e.g. avaible metabolite concentrations
dryweight	A number giving the current dryweight of the organism.
tstep	A number giving the time intervals for each simulation step.
scale	A numeric defining the scaling (units for linear programming has to be in certain range)
j	debuging index to track cell
cutoff	value used to define numeric accuracy while interpreting optimization results

Details

The constraints are calculated according to the flux definition as mmol/(gDW*hr) with the parameters dryweight and tstep.

Value

Returns the lower bounds, which carry the constraints and names of relevant reactions.

See Also

Organism-class

Examples

data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
org <- Organism(Ec_core,deathrate=0.05,
           minweight=0.05,growtype="exponential") #initialize an organism
lobnds <- constrain(org,org@medium,org@lbnd[org@medium],1,1,1,1,1)

euba/BacArena documentation built on Aug. 29, 2024, 11:15 p.m.