constrain {BacArena} | R Documentation |
The generic function constrain
changes the constraints of the model representation of an organism.
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)
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 |
The constraints are calculated according to the flux definition as mmol/(gDW*hr) with the parameters dryweight
and tstep
.
Returns the lower bounds, which carry the constraints and names of relevant reactions.
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)