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Add or modify a reaction

Source: R/model_modifications.R
addReact.Rd

The function can be used to add or modify a reaction in an existing model.

Usage

addReact(
  model,
  id,
  met,
  Scoef,
  reversible = FALSE,
  lb = 0,
  ub = COBRAR_SETTINGS("MAXIMUM"),
  obj = 0,
  subsystem = NA,
  subsystemName = NA,
  gprAssoc = NA,
  reactName = NA,
  metName = NA,
  metComp = NA,
  metCharge = NA,
  metChemicalFormula = NA,
  CVTerms = NA,
  SBOTerm = "guess"
)

Arguments

model

Model of class ModelOrg

id

Character for the reaction ID

met

Character vector providing the IDs of metabolites that participate in the reaction

Scoef

Numeric vector (same length as met) of stoichiometric coefficients for the metabolites in met. The value in Scoef[i] is the stoichiometric coefficient of the metabolite in met[i].

reversible

This option has now effect and is only here for legacy reasons. Whether a reaction is reversible or not is inferred by cobrar based on the lower and upper bounds.

lb, ub

Single numeric values that define the lower and upper flux limits, respectively.

obj

Single numeric value for the coefficient of the reaction in the objective function.

subsystem

A vector of character strings containing the sub system IDs to which the reaction belongs.

subsystemName

A character vector (same length as subsystem) for the names of the subsystems. If the subsystem is already part of the model and you do not want to change its name, just use NA the corresponding entry.

gprAssoc

A single character string giving the Gene-Product-Reaction (GPR) association for the reaction. If NA, no GRP association is created.

reactName

A single character string giving the name for the reaction. If NA, the value of argument id is used.

metName

A vector of character strings of the same length as met containing the metabolites names for the metabolites given in argument met.

metComp

A vector of character strings of the same length as met specifying the compartment IDs for the metabolites given in argument met.

metCharge

A numeric vector of the same length as met defining the charges for the metabolites given in argument met.

metChemicalFormula

A character vector of the same length as met defining the chemical formulas for the metabolites given in argument met.

CVTerms

Cross-references to other resources.

SBOTerm

A term ID from the Systems Biology Ontology. If 'guess', the SBO will be inferred from the reaction details.

Details

If you want to use the function to update data of a pre-existing reaction but not its stoichiometry, use NA for the parameters 'met' and 'Scoeff'. If the reaction is already part of the model, any reaction value (e.g., lb, ub, reactName), that is set to NA has the effect that the old value will be used. If the reaction is already part of the model, and values for the parameter subsystem are provided, all previous set subsystem associations of the reaction will be removed. If metabolites or subsystems are not part of the model yet, they will be added.

Examples

# This example adds the 4-aminobutyrate degradation pathway to the E. coli
# core metabolic model
fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
mod <- readSBMLmod(fpath)

fba(mod)
#> Algorithm:              FBA 
#> Solver status:          solution is optimal 
#> Optimization status:    optimization process was successful 
#> Objective fct. value:   0.8739215 
#> Secondary objective:    NA 

# 4abut transport: 4abut_e + h_e <=> 4abut_c + h_c
mod <- addReact(mod, id = "ABUTt", Scoef = c(-1,-1,1,1),
                met = c("4abut_e","h_e","4abut_c","h_c"), reversible = TRUE,
                lb = -1000, ub = 1000,
                reactName = "4-aminobutyrate transport in via proton symport",
                metName = c("4-aminobutyrate",NA, "4-aminobutyrate",NA),
                metComp = c("e","e","c","c"), metCharge = c(0,NA,0,NA),
                metChemicalFormula = c("C4H9NO2",NA,"C4H9NO2",NA))

# exchange reaction for 4abut (with 1.5 mmol/gDW/hr availability)
mod <- addReact(mod, id = "EX_4abut_e", Scoef = c(-1), met = "4abut_e",
                lb = -1.5, ub = 1000, reactName = "4-aminobutyrate exchange")

# 4abut amninotransferase (EC 2.6.1.19)
mod <- addReact(mod, id = "ABTA", Scoef = c(-1,-1,1,1),
                met = c("4abut_c","akg_c","glu__L_c","sucsal_c"),
                lb = 0,
                reactName = "4-aminobutyrate transaminase",
                metName = c(NA,NA,NA,"Succinic semialdehyde"),
                metComp = c(NA,NA,NA,"c"), metCharge = c(NA,NA,NA,-1),
                metChemicalFormula = c(NA,NA,NA,"C4H5O3"),
                subsystem = "GABAdegr", subsystemName = "4-aminobutyrate degradation",
                CVTerms = "bqbiol_is;http://identifiers.org/ec-code/2.6.1.19",
                gprAssoc = "b2662 | b1302")

# Succinate-semialdehyde dehydrogenase (NAD) (EC 1.2.1.24)
mod <- addReact(mod, id = "SSALx", Scoef = c(-1,-1,-1,2,1,1),
                met = c("h2o_c","nad_c","sucsal_c","h_c","nadh_c","succ_c"),
                lb = 0,
                reactName = "Succinate-semialdehyde dehydrogenase (NAD)",
                subsystem = "GABAdegr",
                CVTerms = "bqbiol_is;http://identifiers.org/ec-code/1.2.1.24",
                gprAssoc = "b1525")

printReaction(mod, "SSALx")
#> [1] "(1) H2O + (1) NAD + (1) Succinic semialdehyde --> (2) H+ + (1) NADH + (1) Succinate"

fba(mod)
#> Algorithm:              FBA 
#> Solver status:          solution is optimal 
#> Optimization status:    optimization process was successful 
#> Objective fct. value:   0.9674959 
#> Secondary objective:    NA