# Efficient Constrained Based Modelling

## Documentation for package ‘sybil’ version 2.1.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P R S T U V W Y misc

sybil-package | sybil - Efficient Constrained Based Modelling in R

## -- A --

addAlgorithm | Add a New Algorithm Name to sybil
addCols | Add Columns to an Optimization Problem
addCols-method | Add Columns to an Optimization Problem
addCols-methods | Add Columns to an Optimization Problem
addColsToProb | Add New Columns (Variables) to an Optimization Problem
addColsToProb-method | Add New Columns (Variables) to an Optimization Problem
addColsToProb-methods | Add New Columns (Variables) to an Optimization Problem
addExchReact | Add Exchange Reactions to a Model
addReact | Add/Change Reactions in a Model
addReact-method | Add/Change Reactions in a Model
addRows | Add Rows to an Optimization Problem
addRows-method | Add Rows to an Optimization Problem
addRows-methods | Add Rows to an Optimization Problem
addRowsCols | Add Rows and Columns to an Optimization Problem
addRowsCols-method | Add Rows and Columns to an Optimization Problem
addRowsCols-methods | Add Rows and Columns to an Optimization Problem
addRowsToProb | Add New Rows (Constraints) to an Optimization Problem
addRowsToProb-method | Add New Rows (Constraints) to an Optimization Problem
addRowsToProb-methods | Add New Rows (Constraints) to an Optimization Problem
addSolver | Add a New Mathematical Programming Solver to sybil
ALGORITHM | Set and Get sybil Parameters
algorithm | Class optsol
algorithm-method | Class optsol
algorithm-method | Class '"sysBiolAlg"'
algorithm<- | Class optsol
algorithm<--method | Class optsol
algorithm<--method | Class '"sysBiolAlg"'
alg_par | Class '"sysBiolAlg"'
alg_par-method | Class optsol
alg_par-method | Class '"sysBiolAlg"'
alg_par<- | Class '"sysBiolAlg"'
alg_par<--method | Class optsol
alg_par<--method | Class '"sysBiolAlg"'
allGenes | Structure of Class "modelorg"
allGenes-method | Structure of Class "modelorg"
allGenes<- | Structure of Class "modelorg"
allGenes<--method | Structure of Class "modelorg"
applyChanges | Generic Function to Apply Changes to Objects of Class sysBiolAlg
applyChanges-method | Generic Function to Apply Changes to Objects of Class sysBiolAlg
applyChanges-methods | Generic Function to Apply Changes to Objects of Class sysBiolAlg

## -- B --

backupProb | Copies a Problem Object to a New Problem Object
backupProb-method | Copies a Problem Object to a New Problem Object
backupProb-methods | Copies a Problem Object to a New Problem Object
blocked | Class '"optsol_blockedReact"'
blocked-method | Class '"optsol_blockedReact"'
blocked<- | Class '"optsol_blockedReact"'
blocked<--method | Class '"optsol_blockedReact"'
blockedReact | Find Blocked Reactions in a Metabolic Network
blReact | Class '"optsol_fluxVar"'
blReact-method | Class '"optsol_fluxVar"'

## -- C --

changeBounds | Change Variable Bounds in a Metabolic Network
changeColsBnds | Change Column (Variable) Bounds in the Optimization Problem
changeColsBnds-method | Change Column (Variable) Bounds in the Optimization Problem
changeColsBnds-methods | Change Column (Variable) Bounds in the Optimization Problem
changeColsBndsObjCoefs | Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem
changeColsBndsObjCoefs-method | Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem
changeColsBndsObjCoefs-methods | Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem
changeGPR | Check and Change the GPR Rules
changeMatrixRow | Change a Row in the Constraint Matrix of the Optimization Problem
changeMatrixRow-method | Change a Row in the Constraint Matrix of the Optimization Problem
changeMatrixRow-methods | Change a Row in the Constraint Matrix of the Optimization Problem
changeMaxObj | Class '"sysBiolAlg_mtf"'
changeMaxObj-method | Class '"sysBiolAlg_mtf"'
changeObjCoefs | Change Column (Variable) Objective Coefficients in the Optimization Problem
changeObjCoefs-method | Change Column (Variable) Objective Coefficients in the Optimization Problem
changeObjCoefs-methods | Change Column (Variable) Objective Coefficients in the Optimization Problem
changeObjFunc | Sets/changes the Objective Function
changeRowsBnds | Change Row Bounds in the Optimization Problem
changeRowsBnds-method | Change Row Bounds in the Optimization Problem
changeRowsBnds-methods | Change Row Bounds in the Optimization Problem
changeUptake | Change Uptake Reactions
changeUptake-method | Change Uptake Reactions
changeUptake-methods | Change Uptake Reactions
checkAlgorithm | Check Algorithm
checkDefaultMethod | Validate Solver and Method
checkOptSol | Summarized Information About an Object of Class Optsol
checkOptSol-method | Summarized Information About an Object of Class Optsol
checkOptSol-methods | Summarized Information About an Object of Class Optsol
checkReactId | Check if a Reaction Id is Valid
checksol | Structure of the Class "checksol"
checksol-class | Structure of the Class "checksol"
checkSolStat | Class '"optObj"'
checkStat | Class optsol
checkStat-method | Class optsol
checkVersion | checks Version of modelorg
checkVersion,modelorg | checks Version of modelorg
checkVersion-method | checks Version of modelorg
checkVersion-methods | checks Version of modelorg
chlb | Class '"optsol_fluxdel"'
chlb-method | Class '"optsol_fluxdel"'
chlb<- | Class '"optsol_fluxdel"'
chlb<--method | Class '"optsol_fluxdel"'
chub | Class '"optsol_fluxdel"'
chub-method | Class '"optsol_fluxdel"'
chub<- | Class '"optsol_fluxdel"'
chub<--method | Class '"optsol_fluxdel"'
clpPtr-class | Class '"optObj"'
cmd | Class '"ppProc"'
cmd-method | Class '"ppProc"'
cmd<- | Class '"ppProc"'
cmd<--method | Class '"ppProc"'
comp_attr | Structure of Class "modelorg"
comp_attr-method | Structure of Class "modelorg"
comp_attr<- | Structure of Class "modelorg"
comp_attr<--method | Structure of Class "modelorg"
cplexPointer-class | Class '"optObj"'
cplexPtr-class | Class '"optObj"'
ctrlfl | Class '"optsol_robAna"'
ctrlfl-method | Class '"optsol_phpp"'
ctrlfl-method | Class '"optsol_robAna"'
ctrlfl<- | Class '"optsol_robAna"'
ctrlfl<--method | Class '"optsol_phpp"'
ctrlfl<--method | Class '"optsol_robAna"'
ctrlr | Class '"optsol_robAna"'
ctrlr-method | Class '"optsol_robAna"'
ctrlr<- | Class '"optsol_robAna"'
ctrlr<--method | Class '"optsol_robAna"'

## -- D --

deadEndMetabolites | Identify Dead End Metabolites
deadEndMetabolites-method | Identify Dead End Metabolites
deadEndMetabolites-methods | Identify Dead End Metabolites
deleted | Class '"optsol_fluxdel"'
deleted-method | Class '"optsol_fluxdel"'
deleted-method | Class '"optsol_genedel"'
delProb | Free Memory Associated to the Pointer to the Problem Object
delProb-method | Free Memory Associated to the Pointer to the Problem Object
delProb-methods | Free Memory Associated to the Pointer to the Problem Object
dels | Class '"optsol_fluxdel"'
dels-method | Class '"optsol_fluxdel"'
dels<- | Class '"optsol_fluxdel"'
dels<--method | Class '"optsol_fluxdel"'
didFoot | Class '"sybilLog"'
didFoot-method | Class '"sybilLog"'
didFoot<- | Class '"sybilLog"'
didFoot<--method | Class '"sybilLog"'
dim-method | Structure of Class "modelorg"
dim-method | Class '"optObj"'
doubleFluxDel | Double Flux Deletion Experiment
doubleGeneDel | Double Gene Deletion Experiment
doubleReact | Identifies Identical Reactions

## -- E --

EasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
Ec_core | Escherichia coli Core Metabolic Model
editEnvir | Environment Editor for Metabolic Networks
emsg | Class '"sybilError"'
emsg-method | Class '"sybilError"'
emsg<- | Class '"sybilError"'
emsg<--method | Class '"sybilError"'
enum | Class '"sybilError"'
enum-method | Class '"sybilError"'
enum<- | Class '"sybilError"'
enum<--method | Class '"sybilError"'
exit_code | Structure of the Class "checksol"
exit_code-method | Structure of the Class "checksol"
exit_code<- | Structure of the Class "checksol"
exit_code<--method | Structure of the Class "checksol"
exit_meaning | Structure of the Class "checksol"
exit_meaning-method | Structure of the Class "checksol"
exit_meaning<- | Structure of the Class "checksol"
exit_meaning<--method | Structure of the Class "checksol"
exit_num | Structure of the Class "checksol"
exit_num-method | Structure of the Class "checksol"
exit_num<- | Structure of the Class "checksol"
exit_num<--method | Structure of the Class "checksol"
ex_met | Class '"summaryOptsol"'
ex_met-method | Class '"summaryOptsol"'
ex_val | Class '"summaryOptsol"'
ex_val-method | Class '"summaryOptsol"'

## -- F --

fba | Class '"sysBiolAlg_fba"'
fbaEasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
fenc | Class '"sybilLog"'
fenc-method | Class '"sybilLog"'
fenc<- | Class '"sybilLog"'
fenc<--method | Class '"sybilLog"'
fh | Class '"sybilLog"'
fh-method | Class '"sybilLog"'
fh<- | Class '"sybilLog"'
fh<--method | Class '"sybilLog"'
file-class | Class '"sybilLog"'
findExchReact | Find Exchange Reactions
fldind | Class optsol
fldind-method | Class optsol
fldind-method | Class '"sysBiolAlg"'
fldind<- | Class optsol
fldind<--method | Class optsol
fldind<--method | Class '"sysBiolAlg"'
fluxdels | Class '"optsol_genedel"'
fluxdels-method | Class '"optsol_genedel"'
fluxdels<- | Class '"optsol_genedel"'
fluxdels<--method | Class '"optsol_genedel"'
fluxdist | Class optsol
fluxdist-method | Class optsol
fluxdist<- | Class optsol
fluxdist<--method | Class optsol
fluxDistribution | Class '"fluxDistribution"'
fluxDistribution-class | Class '"fluxDistribution"'
fluxes | Class optsol
fluxes-method | Class '"fluxDistribution"'
fluxes-method | Class optsol
fluxes<- | Class optsol
fluxes<--method | Class '"fluxDistribution"'
fluxes<--method | Class optsol
fluxVar | Flux Variability Analysis
fname | Class '"sybilLog"'
fname-method | Class '"sybilLog"'
fname<- | Class '"sybilLog"'
fname<--method | Class '"sybilLog"'
fpath | Class '"sybilLog"'
fpath-method | Class '"sybilLog"'
fpath<- | Class '"sybilLog"'
fpath<--method | Class '"sybilLog"'
fv | Class '"sysBiolAlg_fv"'

## -- G --

geneDel | Get Gene-Reaction Association
geneDeletion | Gene Deletion Experiments
genes | Structure of Class "modelorg"
genes-method | Structure of Class "modelorg"
genes<- | Structure of Class "modelorg"
genes<--method | Structure of Class "modelorg"
getColPrim | Get Primal Value of Variables After Optimization
getColPrim-method | Get Primal Value of Variables After Optimization
getColPrim-methods | Get Primal Value of Variables After Optimization
getColsLowBnds | Get Lower Bounds of the Columns (Variables) of the Optimization Problem
getColsLowBnds-method | Get Lower Bounds of the Columns (Variables) of the Optimization Problem
getColsLowBnds-methods | Get Lower Bounds of the Columns (Variables) of the Optimization Problem
getColsNames | Retrieve Variable Names
getColsNames-method | Retrieve Variable Names
getColsNames-methods | Retrieve Variable Names
getColsUppBnds | Get Upper Bounds of the Columns (Variables) of the Optimization Problem
getColsUppBnds-method | Get Upper Bounds of the Columns (Variables) of the Optimization Problem
getColsUppBnds-methods | Get Upper Bounds of the Columns (Variables) of the Optimization Problem
getFluxDist | Retrieve Flux Distribution
getFluxDist-method | Retrieve Flux Distribution
getFluxDist-methods | Retrieve Flux Distribution
getMeanReturn | Class '"optObj"'
getMeanStatus | Class '"optObj"'
getNetFlux | Class '"netFlux"'
getNumCols | Get Number of Columns (Variables) of the Optimization Problem
getNumCols-method | Get Number of Columns (Variables) of the Optimization Problem
getNumCols-methods | Get Number of Columns (Variables) of the Optimization Problem
getNumNnz | Retrieve the Number of Non-Zero Elements of the Constraint Matrix
getNumNnz-method | Retrieve the Number of Non-Zero Elements of the Constraint Matrix
getNumNnz-methods | Retrieve the Number of Non-Zero Elements of the Constraint Matrix
getNumRows | Get Number of Rows (Constraints) of the Optimization Problem
getNumRows-method | Get Number of Rows (Constraints) of the Optimization Problem
getNumRows-methods | Get Number of Rows (Constraints) of the Optimization Problem
getObjCoefs | Get Objective Coefficients of the Optimization Problem
getObjCoefs-method | Get Objective Coefficients of the Optimization Problem
getObjCoefs-methods | Get Objective Coefficients of the Optimization Problem
getObjDir | Get Direction of Optimization.
getObjDir-method | Get Direction of Optimization.
getObjDir-methods | Get Direction of Optimization.
getObjVal | Get Value of the Objective Function After Optimization
getObjVal-method | Get Value of the Objective Function After Optimization
getObjVal-methods | Get Value of the Objective Function After Optimization
getReaction | Functions to subset and merge modelorg objects.
getReaction-method | Functions to subset and merge modelorg objects.
getRedCosts | Get Reduced Costs of all Variables After Optimization
getRedCosts-method | Get Reduced Costs of all Variables After Optimization
getRedCosts-method | Class '"optsol_phpp"'
getRedCosts-methods | Get Reduced Costs of all Variables After Optimization
getRowsLowBnds | Get Lower Bounds of the Rows (Constraints) of the Optimization Problem
getRowsLowBnds-method | Get Lower Bounds of the Rows (Constraints) of the Optimization Problem
getRowsLowBnds-methods | Get Lower Bounds of the Rows (Constraints) of the Optimization Problem
getRowsNames | Retrieve Constraint Names
getRowsNames-method | Retrieve Constraint Names
getRowsNames-methods | Retrieve Constraint Names
getRowsUppBnds | Get Upper Bounds of the Rows (Constraints) of the Optimization Problem
getRowsUppBnds-method | Get Upper Bounds of the Rows (Constraints) of the Optimization Problem
getRowsUppBnds-methods | Get Upper Bounds of the Rows (Constraints) of the Optimization Problem
getSolStat | Get Solution Status After Optimization
getSolStat-method | Get Solution Status After Optimization
getSolStat-methods | Get Solution Status After Optimization
getSolverParm | Retrieve Current Parameter Settings Used By The Optimization Software
getSolverParm-method | Retrieve Current Parameter Settings Used By The Optimization Software
getSolverParm-methods | Retrieve Current Parameter Settings Used By The Optimization Software
getsybilenv | Print sybil Environment
glpkPtr-class | Class '"optObj"'
gpr | Structure of Class "modelorg"
gpr-method | Structure of Class "modelorg"
gpr<- | Structure of Class "modelorg"
gpr<--method | Structure of Class "modelorg"
gprRule | Structure of Class "modelorg"
gprRule-method | Structure of Class "modelorg"
gprRule<- | Structure of Class "modelorg"
gprRule<--method | Structure of Class "modelorg"
gprRules | Structure of Class "modelorg"
gprRules-method | Structure of Class "modelorg"
gprRules<- | Structure of Class "modelorg"
gprRules<--method | Structure of Class "modelorg"

## -- H --

hasEffect | Class '"optsol_genedel"'
hasEffect-method | Class '"optsol_genedel"'
hasEffect<- | Class '"optsol_genedel"'
hasEffect<--method | Class '"optsol_genedel"'

## -- I --

image-method | Class '"summaryOptsol"'
ind | Class '"ppProc"'
ind-method | Class '"ppProc"'
ind<- | Class '"ppProc"'
ind<--method | Class '"ppProc"'
initProb | Initialize Problem Object
initProb-method | Initialize Problem Object
initProb-methods | Initialize Problem Object
irrev | Class for Metabolic Networks in Irreversible Format.
irrev-method | Class for Metabolic Networks in Irreversible Format.
irrev2rev | Class for Metabolic Networks in Irreversible Format.
irrev2rev-method | Class for Metabolic Networks in Irreversible Format.
irrev2rev<- | Class for Metabolic Networks in Irreversible Format.
irrev2rev<--method | Class for Metabolic Networks in Irreversible Format.
irrev<- | Class for Metabolic Networks in Irreversible Format.
irrev<--method | Class for Metabolic Networks in Irreversible Format.

## -- L --

length-method | Class '"netFlux"'
length-method | Class optsol
length-method | Structure of Class "reactId"
lethal | Class '"optsol_fluxdel"'
lethal-method | Class '"optsol_fluxdel"'
lmoma | Class '"sysBiolAlg_lmoma"'
loadLPprob | Load Data to Optimization Problem
loadLPprob-method | Load Data to Optimization Problem
loadLPprob-methods | Load Data to Optimization Problem
loadMatrixPerColumnLPSOLVE | Class '"optObj_lpSolveAPI"'
loadQobj | Load Quadratic Part of the Objective Function to the Optimization Problem
loadQobj-method | Load Quadratic Part of the Objective Function to the Optimization Problem
loadQobj-methods | Load Quadratic Part of the Objective Function to the Optimization Problem
logCall | Class '"sybilLog"'
logCall-method | Class '"sybilLog"'
logClose<- | Class '"sybilLog"'
logClose<--method | Class '"sybilLog"'
logComment | Class '"sybilLog"'
logComment-method | Class '"sybilLog"'
logError | Class '"sybilLog"'
logError-method | Class '"sybilLog"'
logFH | Class '"sybilLog"'
logFH-method | Class '"sybilLog"'
logFileFH | Class '"sybilLog"'
logFoot<- | Class '"sybilLog"'
logFoot<--method | Class '"sybilLog"'
logHead | Class '"sybilLog"'
logHead-method | Class '"sybilLog"'
loglevel | Class '"sybilLog"'
loglevel-method | Class '"sybilLog"'
loglevel<- | Class '"sybilLog"'
loglevel<--method | Class '"sybilLog"'
logMessage | Class '"sybilLog"'
logMessage-method | Class '"sybilLog"'
logOptimization | Class '"sybilLog"'
logOptimization-method | Class '"sybilLog"'
logOptimizationTH | Class '"sybilLog"'
logOptimizationTH-method | Class '"sybilLog"'
logStep<- | Class '"sybilLog"'
logStep<--method | Class '"sybilLog"'
logWarning | Class '"sybilLog"'
logWarning-method | Class '"sybilLog"'
lowbnd | Structure of Class "modelorg"
lowbnd-method | Structure of Class "modelorg"
lowbnd-method | Class '"reactId_Exch"'
lowbnd<- | Structure of Class "modelorg"
lowbnd<--method | Structure of Class "modelorg"
lowbnd<--method | Class '"reactId_Exch"'
lpExtPtr-class | Class '"optObj"'
lp_dir | Class optsol
lp_dir-method | Class optsol
lp_dir<- | Class optsol
lp_dir<--method | Class optsol
lp_num_cols | Class optsol
lp_num_cols-method | Class optsol
lp_num_cols<- | Class optsol
lp_num_cols<--method | Class optsol
lp_num_rows | Class optsol
lp_num_rows-method | Class optsol
lp_num_rows<- | Class optsol
lp_num_rows<--method | Class optsol
lp_obj | Class optsol
lp_obj-method | Class optsol
lp_obj<- | Class optsol
lp_obj<--method | Class optsol
lp_ok | Class optsol
lp_ok-method | Class optsol
lp_ok<- | Class optsol
lp_ok<--method | Class optsol
lp_stat | Class optsol
lp_stat-method | Class optsol
lp_stat<- | Class optsol
lp_stat<--method | Class optsol
lstname | Class '"sybilLog"'
lstname-method | Class '"sybilLog"'

## -- M --

makeOptsolMO | Constructor Function for Objects of Class 'optsol_optimizeProb'.
matchrev | Class for Metabolic Networks in Irreversible Format.
matchrev-method | Class for Metabolic Networks in Irreversible Format.
matchrev<- | Class for Metabolic Networks in Irreversible Format.
matchrev<--method | Class for Metabolic Networks in Irreversible Format.
MAXIMUM | Set and Get sybil Parameters
maxSol | Class '"optsol_blockedReact"'
maxSol-method | Class '"optsol_blockedReact"'
maxSol-method | Class '"optsol_fluxVar"'
mergeReact2Modelorg | Functions to subset and merge modelorg objects.
METHOD | Set and Get sybil Parameters
method | Class optsol
method-method | Class '"optObj"'
method-method | Class optsol
method<- | Class optsol
method<--method | Class optsol
met_attr | Structure of Class "modelorg"
met_attr-method | Structure of Class "modelorg"
met_attr<- | Structure of Class "modelorg"
met_attr<--method | Structure of Class "modelorg"
met_comp | Structure of Class "modelorg"
met_comp-method | Structure of Class "modelorg"
met_comp<- | Structure of Class "modelorg"
met_comp<--method | Structure of Class "modelorg"
met_de | Structure of Class "modelorg"
met_de-method | Structure of Class "modelorg"
met_de<- | Structure of Class "modelorg"
met_de<--method | Structure of Class "modelorg"
met_id | Structure of Class "modelorg"
met_id-method | Structure of Class "modelorg"
met_id-method | Class '"reactId_Exch"'
met_id<- | Structure of Class "modelorg"
met_id<--method | Structure of Class "modelorg"
met_id<--method | Class '"reactId_Exch"'
met_name | Structure of Class "modelorg"
met_name-method | Structure of Class "modelorg"
met_name<- | Structure of Class "modelorg"
met_name<--method | Structure of Class "modelorg"
met_num | Structure of Class "modelorg"
met_num-method | Structure of Class "modelorg"
met_num<- | Structure of Class "modelorg"
met_num<--method | Structure of Class "modelorg"
met_pos | Class '"reactId_Exch"'
met_pos-method | Class '"reactId_Exch"'
met_pos<- | Class '"reactId_Exch"'
met_pos<--method | Class '"reactId_Exch"'
met_single | Structure of Class "modelorg"
met_single-method | Structure of Class "modelorg"
met_single<- | Structure of Class "modelorg"
met_single<--method | Structure of Class "modelorg"
minSol | Class '"optsol_blockedReact"'
minSol-method | Class '"optsol_blockedReact"'
minSol-method | Class '"optsol_fluxVar"'
mod2irrev | Produces a Model in Irreversible Format
modelorg | Structure of Class "modelorg"
modelorg-class | Structure of Class "modelorg"
modelorg2ExPA | Write an Instance of Class modelorg to File in ExPA Format
modelorg2tsv | Write an Instance of Class modelorg to File
modelorg_irrev | Class for Metabolic Networks in Irreversible Format.
modelorg_irrev-class | Class for Metabolic Networks in Irreversible Format.
mod_attr | Structure of Class "modelorg"
mod_attr-method | Structure of Class "modelorg"
mod_attr<- | Structure of Class "modelorg"
mod_attr<--method | Structure of Class "modelorg"
mod_compart | Structure of Class "modelorg"
mod_compart-method | Structure of Class "modelorg"
mod_compart<- | Structure of Class "modelorg"
mod_compart<--method | Structure of Class "modelorg"
mod_desc | Structure of Class "modelorg"
mod_desc-method | Structure of Class "modelorg"
mod_desc<- | Structure of Class "modelorg"
mod_desc<--method | Structure of Class "modelorg"
mod_id | Structure of Class "modelorg"
mod_id-method | Structure of Class "modelorg"
mod_id-method | Class optsol
mod_id-method | Structure of Class "reactId"
mod_id-method | Class '"summaryOptsol"'
mod_id<- | Structure of Class "modelorg"
mod_id<--method | Structure of Class "modelorg"
mod_id<--method | Class optsol
mod_id<--method | Structure of Class "reactId"
mod_id<--method | Class '"summaryOptsol"'
mod_key | Structure of Class "modelorg"
mod_key-method | Structure of Class "modelorg"
mod_key-method | Class optsol
mod_key-method | Structure of Class "reactId"
mod_key-method | Class '"summaryOptsol"'
mod_key<- | Structure of Class "modelorg"
mod_key<--method | Structure of Class "modelorg"
mod_key<--method | Class optsol
mod_key<--method | Structure of Class "reactId"
mod_key<--method | Class '"summaryOptsol"'
mod_name | Structure of Class "modelorg"
mod_name-method | Structure of Class "modelorg"
mod_name<- | Structure of Class "modelorg"
mod_name<--method | Structure of Class "modelorg"
mod_obj | Class optsol
mod_obj-method | Class optsol
mod_obj-method | Class '"summaryOptsol"'
mod_obj<- | Class '"summaryOptsol"'
mod_obj<--method | Class '"summaryOptsol"'
moma | Class '"sysBiolAlg_moma"'
mtf | Class '"sysBiolAlg_mtf"'
mtfEasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
multiDel | Parallel Support for sybil

## -- N --

nc | Class '"sysBiolAlg"'
nc-method | Class '"sysBiolAlg"'
nc<- | Class '"sysBiolAlg"'
nc<--method | Class '"sysBiolAlg"'
netFlux | Class '"netFlux"'
netFlux-class | Class '"netFlux"'
nfluxes | Class optsol
nfluxes-method | Class optsol
nnzero-method | Class '"fluxDistribution"'
nnzero-method | Class '"summaryOptsol"'
nr | Class '"sysBiolAlg"'
nr-method | Class '"sysBiolAlg"'
nr<- | Class '"sysBiolAlg"'
nr<--method | Class '"sysBiolAlg"'
num_of_fluxes | Class '"fluxDistribution"'
num_of_fluxes-method | Class '"fluxDistribution"'
num_of_prob | Class optsol
num_of_prob-method | Structure of the Class "checksol"
num_of_prob-method | Class optsol
num_of_prob<- | Class optsol
num_of_prob<--method | Structure of the Class "checksol"
num_of_prob<--method | Class optsol
nvar | Class '"fluxDistribution"'
nvar-method | Class '"fluxDistribution"'
nzeros | Class '"summaryOptsol"'
nzeros-method | Class '"summaryOptsol"'

## -- O --

obj_coef | Structure of Class "modelorg"
obj_coef-method | Structure of Class "modelorg"
obj_coef-method | Class optsol
obj_coef<- | Structure of Class "modelorg"
obj_coef<--method | Structure of Class "modelorg"
obj_coef<--method | Class optsol
obj_func | Class optsol
obj_func-method | Class optsol
obj_func<- | Class optsol
obj_func<--method | Class optsol
oneFluxDel | Single Flux Deletion Experiment
oneGeneDel | Single Gene Deletion Experiment
onlyChangeGPR | Change the GPR Rules
onlyCheckGPR | Check the GPR Rules
optimizeProb | Optimize Problem Object
optimizeProb-method | Optimize Problem Object
optimizeProb-methods | Optimize Problem Object
optimizer | Performs Series of Optimizations
optObj | General Constructor Function For Objects of Class 'optObj'
optObj-class | Class '"optObj"'
optObj_clpAPI-class | Class '"optObj_clpAPI"'
optObj_cplexAPI-class | Class '"optObj_cplexAPI"'
optObj_glpkAPI-class | Class '"optObj_glpkAPI"'
optObj_lpSolveAPI-class | Class '"optObj_lpSolveAPI"'
optsol | Class optsol
optsol-class | Class optsol
optsol_blockedReact-class | Class '"optsol_blockedReact"'
optsol_fluxdel-class | Class '"optsol_fluxdel"'
optsol_fluxVar-class | Class '"optsol_fluxVar"'
optsol_genedel-class | Class '"optsol_genedel"'
optsol_optimizeProb-class | Class '"optsol_optimizeProb"'
optsol_phpp-class | Class '"optsol_phpp"'
optsol_robAna-class | Class '"optsol_robAna"'
OPT_DIRECTION | Set and Get sybil Parameters

## -- P --

pa | Class '"ppProc"'
pa-method | Class '"ppProc"'
pa<- | Class '"ppProc"'
pa<--method | Class '"ppProc"'
PATH_TO_MODEL | Set and Get sybil Parameters
phpp | Phenotypic Phase Plane Analysis
plot-method | Class '"fluxDistribution"'
plot-method | Class optsol
plot-method | Class '"optsol_fluxVar"'
plot-method | Class '"optsol_phpp"'
plot-method | Class '"optsol_robAna"'
plot-method | Class '"summaryOptsol"'
plotRangeVar | Class '"optsol_fluxVar"'
plotRangeVar-method | Class '"optsol_fluxVar"'
pointerToProb | Class '"optObj"'
pointerToProb-class | Class '"optObj"'
postProc | Class '"optsol_optimizeProb"'
postProc-method | Class '"optsol_optimizeProb"'
postProc<- | Class '"optsol_optimizeProb"'
postProc<--method | Class '"optsol_optimizeProb"'
ppProc | Class '"ppProc"'
ppProc-class | Class '"ppProc"'
preProc | Class '"optsol_optimizeProb"'
preProc-method | Class '"optsol_optimizeProb"'
preProc<- | Class '"optsol_optimizeProb"'
preProc<--method | Class '"optsol_optimizeProb"'
printExchange | Class '"summaryOptsol"'
printExchange-method | Class '"summaryOptsol"'
printMetabolite | Print Rows of the Stoichiometric Matrix
printMetabolite-method | Print Rows of the Stoichiometric Matrix
printMetabolite-methods | Print Rows of the Stoichiometric Matrix
printObjFunc | Structure of Class "modelorg"
printObjFunc-method | Structure of Class "modelorg"
printReaction | Print Columns of the Stoichiometric Matrix
printReaction-method | Print Columns of the Stoichiometric Matrix
printReaction-methods | Print Columns of the Stoichiometric Matrix
problem | Class '"sysBiolAlg"'
problem-method | Class '"sysBiolAlg"'
probType | Class '"optObj"'
probType-method | Class '"optObj"'
promptSysBiolAlg | Generate A Skeletal Structure of Subclasses of sysBiolAlg

## -- R --

rate | Class '"netFlux"'
rate-method | Class '"netFlux"'
react | Structure of Class "modelorg"
react-class | Structure of Class "modelorg"
react-method | Class '"optsol_blockedReact"'
react-method | Class '"optsol_fluxVar"'
react<- | Class '"optsol_blockedReact"'
react<--method | Class '"optsol_blockedReact"'
react<--method | Class '"optsol_fluxVar"'
reactId | Structure of Class "reactId"
reactId-class | Structure of Class "reactId"
reactId_Exch | Class '"reactId_Exch"'
reactId_Exch-class | Class '"reactId_Exch"'
react_attr | Structure of Class "modelorg"
react_attr-method | Structure of Class "modelorg"
react_attr<- | Structure of Class "modelorg"
react_attr<--method | Structure of Class "modelorg"
react_de | Structure of Class "modelorg"
react_de-method | Structure of Class "modelorg"
react_de<- | Structure of Class "modelorg"
react_de<--method | Structure of Class "modelorg"
react_id | Structure of Class "modelorg"
react_id-method | Structure of Class "modelorg"
react_id-method | Class '"netFlux"'
react_id-method | Class optsol
react_id-method | Structure of Class "reactId"
react_id<- | Structure of Class "modelorg"
react_id<--method | Structure of Class "modelorg"
react_id<--method | Class '"netFlux"'
react_id<--method | Class optsol
react_id<--method | Structure of Class "reactId"
react_name | Structure of Class "modelorg"
react_name-method | Structure of Class "modelorg"
react_name<- | Structure of Class "modelorg"
react_name<--method | Structure of Class "modelorg"
react_num | Structure of Class "modelorg"
react_num-method | Structure of Class "modelorg"
react_num<- | Structure of Class "modelorg"
react_num<--method | Structure of Class "modelorg"
react_pos | Structure of Class "reactId"
react_pos-method | Structure of Class "reactId"
react_pos<- | Structure of Class "reactId"
react_pos<--method | Structure of Class "reactId"
react_rev | Structure of Class "modelorg"
react_rev-method | Structure of Class "modelorg"
react_rev<- | Structure of Class "modelorg"
react_rev<--method | Structure of Class "modelorg"
react_single | Structure of Class "modelorg"
react_single-method | Structure of Class "modelorg"
react_single<- | Structure of Class "modelorg"
react_single<--method | Structure of Class "modelorg"
readProb | Read Problem Object From File
readProb-method | Read Problem Object From File
readProb-methods | Read Problem Object From File
readTSVmod | Read a Metabolic Network in a TSV (CSV) Format
resetChanges | Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg
resetChanges-method | Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg
resetChanges-methods | Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg
return_codeLPSOLVE | Class '"optObj_lpSolveAPI"'
rev2irrev | Class for Metabolic Networks in Irreversible Format.
rev2irrev-method | Class for Metabolic Networks in Irreversible Format.
rev2irrev<- | Class for Metabolic Networks in Irreversible Format.
rev2irrev<--method | Class for Metabolic Networks in Irreversible Format.
rmReact | Remove Reactions From a Model
robAna | Robustness Analysis
room | Class '"sysBiolAlg_room"'
rxnGeneMat | Structure of Class "modelorg"
rxnGeneMat-method | Structure of Class "modelorg"
rxnGeneMat<- | Structure of Class "modelorg"
rxnGeneMat<--method | Structure of Class "modelorg"

## -- S --

S | Structure of Class "modelorg"
s | Structure of Class "modelorg"
S-method | Structure of Class "modelorg"
s-method | Structure of Class "modelorg"
S<- | Structure of Class "modelorg"
s<- | Structure of Class "modelorg"
S<--method | Structure of Class "modelorg"
s<--method | Structure of Class "modelorg"
scaleProb | Scaling of the Constraint Matrix of an Optimization Problem
scaleProb-method | Scaling of the Constraint Matrix of an Optimization Problem
scaleProb-methods | Scaling of the Constraint Matrix of an Optimization Problem
sensitivityAnalysis | Sensitivity Analysis
sensitivityAnalysis-method | Sensitivity Analysis
sensitivityAnalysis-methods | Sensitivity Analysis
setColsNames | Set/Change Variable Names
setColsNames-method | Set/Change Variable Names
setColsNames-methods | Set/Change Variable Names
setObjDir | Set Direction of Optimization
setObjDir-method | Set Direction of Optimization
setObjDir-methods | Set Direction of Optimization
setRhsZero | Set Right Hand Side of the Optimization Problem To Zero
setRhsZero-method | Set Right Hand Side of the Optimization Problem To Zero
setRhsZero-methods | Set Right Hand Side of the Optimization Problem To Zero
setRowsNames | Set/Change Constraint Names
setRowsNames-method | Set/Change Constraint Names
setRowsNames-methods | Set/Change Constraint Names
setSolverParm | Set Parameters Used By The Optimization Software
setSolverParm-method | Set Parameters Used By The Optimization Software
setSolverParm-methods | Set Parameters Used By The Optimization Software
show-method | Structure of the Class "checksol"
show-method | Structure of Class "modelorg"
show-method | Class optsol
shrinkMatrix | Get a Subset of Matrix Like Objects
shrinkMatrix-method | Get a Subset of Matrix Like Objects
shrinkMatrix-methods | Get a Subset of Matrix Like Objects
singletonMetabolites | Identify Singleton Metabolites
singletonMetabolites-method | Identify Singleton Metabolites
singletonMetabolites-methods | Identify Singleton Metabolites
Snnz | Structure of Class "modelorg"
Snnz-method | Structure of Class "modelorg"
solveLp | Optimize Problem Object
solveLp-method | Optimize Problem Object
solveLp-methods | Optimize Problem Object
SOLVER | Set and Get sybil Parameters
solver | Class optsol
solver-method | Class '"optObj"'
solver-method | Class optsol
solver<- | Class optsol
solver<--method | Class optsol
SOLVER_CTRL_PARM | Set and Get sybil Parameters
status_code | Structure of the Class "checksol"
status_code-method | Structure of the Class "checksol"
status_code<- | Structure of the Class "checksol"
status_code<--method | Structure of the Class "checksol"
status_meaning | Structure of the Class "checksol"
status_meaning-method | Structure of the Class "checksol"
status_meaning<- | Structure of the Class "checksol"
status_meaning<--method | Structure of the Class "checksol"
status_num | Structure of the Class "checksol"
status_num-method | Structure of the Class "checksol"
status_num<- | Structure of the Class "checksol"
status_num<--method | Structure of the Class "checksol"
stclear | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stexists | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stfirst | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stinit | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stlength | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stlist | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stpop | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stpush | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stseek | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stshift | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stunshift | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
subSys | Structure of Class "modelorg"
subSys-method | Structure of Class "modelorg"
subSys<- | Structure of Class "modelorg"
subSys<--method | Structure of Class "modelorg"
summaryOptsol | Summarize Objects of Class Optsol
summaryOptsol-class | Class '"summaryOptsol"'
sybil | sybil - Efficient Constrained Based Modelling in R
sybil-deprecated | Deprecated Functions and Methods in Package 'sybil'
sybilError | Class '"sybilError"'
sybilError-class | Class '"sybilError"'
sybilLog | Class '"sybilLog"'
sybilLog-class | Class '"sybilLog"'
sybilStack | A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
SYBIL_SETTINGS | Set and Get sybil Parameters
sysBiolAlg | General Constructor Function For Objects of Class 'sysBiolAlg'
sysBiolAlg-class | Class '"sysBiolAlg"'
sysBiolAlg_fba | Class '"sysBiolAlg_fba"'
sysBiolAlg_fba-class | Class '"sysBiolAlg_fba"'
sysBiolAlg_fbaEasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
sysBiolAlg_fbaEasyConstraint-class | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
sysBiolAlg_fv | Class '"sysBiolAlg_fv"'
sysBiolAlg_fv-class | Class '"sysBiolAlg_fv"'
sysBiolAlg_lmoma | Class '"sysBiolAlg_lmoma"'
sysBiolAlg_lmoma-class | Class '"sysBiolAlg_lmoma"'
sysBiolAlg_moma | Class '"sysBiolAlg_moma"'
sysBiolAlg_moma-class | Class '"sysBiolAlg_moma"'
sysBiolAlg_mtf | Class '"sysBiolAlg_mtf"'
sysBiolAlg_mtf-class | Class '"sysBiolAlg_mtf"'
sysBiolAlg_mtfEasyConstraint | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
sysBiolAlg_mtfEasyConstraint-class | Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
sysBiolAlg_room | Class '"sysBiolAlg_room"'
sysBiolAlg_room-class | Class '"sysBiolAlg_room"'

## -- T --

TOLERANCE | Set and Get sybil Parameters

## -- U --

upgradeModelorg | Upgrade modelorg to newer version.
uppbnd | Structure of Class "modelorg"
uppbnd-method | Structure of Class "modelorg"
uppbnd-method | Class '"reactId_Exch"'
uppbnd<- | Structure of Class "modelorg"
uppbnd<--method | Structure of Class "modelorg"
uppbnd<--method | Class '"reactId_Exch"'
uptake | Class '"reactId_Exch"'
uptake-method | Class '"reactId_Exch"'
uptake<- | Class '"reactId_Exch"'
uptake<--method | Class '"reactId_Exch"'
uptMet | Class '"reactId_Exch"'
uptMet-method | Class '"reactId_Exch"'
uptReact | Class '"reactId_Exch"'
uptReact-method | Class '"reactId_Exch"'
USE_NAMES | Set and Get sybil Parameters

## -- V --

verblevel | Class '"sybilLog"'
verblevel-method | Class '"sybilLog"'
verblevel<- | Class '"sybilLog"'
verblevel<--method | Class '"sybilLog"'
version | Structure of Class "modelorg"
version-method | Structure of Class "modelorg"
version<- | Structure of Class "modelorg"
version<--method | Structure of Class "modelorg"

## -- W --

writeProb | Write Problem Object to File
writeProb-method | Write Problem Object to File
writeProb-methods | Write Problem Object to File
wrong_solver_msg | Class '"optObj"'
wrong_type_msg | Class '"optObj"'

## -- Y --

ypd | In Sillico YPD Medium

## -- misc --

[-method | Class '"fluxDistribution"'
[-method | Class '"optsol_fluxdel"'
[-method | Structure of Class "reactId"
[-method | Class '"reactId_Exch"'