Function for constraining the models based on metabolite concentrations
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.