Description Usage Arguments Details Value Author(s) References See Also
given Kcat vector (in 1/Sec), and molecular weights and optionally protein complex stoichiometry formulate a ccFBA problem(Maximize biomass). Improvements over MOMENT: 1 use multifunctioning enzyme constraint. 2use one enzyme (the cheapest) for each reaction catalayzed my multiple isoenzymes and thus eliminate under estimation of rules of form ((A AND B) OR (A AND C)) 3optionally include protein complex stoichiometry
1 2 3 
model 
An object of class 
mod2 
An object of class 
Kcat 
kcat values in unit 1/S. Contains three slots: reaction id,direction(dirxn),value(val) 
MW 
list of molecular weights of all genes, using function calc_MW, in units g/mol 
selected_rxns 
optional parameter used to select a set of reactions not all, list of react_id 
verboseMode 
An integer value indicating the amount of output to stdout:
0: nothing, 1: status messages, 2: like 1 plus with more details,
3: generates files of the LP problem. 
RHS 
the budget C, for EColi 0.27 
objVal 
when not null the problem will be to find the minimum budget that give the specified objective value(biomass) 
solver 
Single character string giving the solver package to use. See

medval 
median of Kcat values , used for missing values 
cpx_stoich 
giving the stoichiometry of complexes: data frame containing at least two columns 'genes','stoich' 'gene' : delimited string of genes(ordered by geneid(e.g bnumber)), 'stoich': number of subunits of each gene in the same order in 'genes' Default: NULL (e.g. all stoichiometry coefficients equal one) 
C_mu_coef 
used to have C as a linear function of mu (biomass) : C = RHS + C_mu_coef*Biomass default 0 (e.g. ignored). 
variable names: g1_x_1: indicates that gene x is in onetoone relation gr_x_r:indicates that gene x catalyzes more than one reaction and this variable is the portion that catalyzes reaction r. gmr_x_cnt: variable for a gene catalyzing more than one reaction (i.e cnt reactions) and this variable is the sum of individual parts. cpx_r: used to represent a complex catalyzing reaction r.
return a LIST,
LHS 
constraint matrix, consists of S matrix and ccFBA constraints 
rlb,rub 
bounds for constraints (i.e rows) 
clb,cub 
bounds for variables (i.e columns) 
rxnkcatRow 
mapping of Kcat values to constraints 
rgst 
complex stoichiometry as returned by 
rxnGeneCol 
rxn_id,gene,Col : used to get MCrowding 
geneCol 
low level structure, used for debugging 
mod_objc_ind 
row index of constraint on FBA model objective 
cc_ind 
capacity constraint index 
Abdelmoneim Amer Desouki
Desouki, Abdelmoneim. "Algorithms for improving the predictive power of flux balance analysis." PhD diss., 2016.
getGpr1iso
, cfba_moment_mr
,simulate_EColi
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