sybil-package	sybil-package
addAlgorithm	addAlgorithm
addCols	addCols-methods
addCols,optObj_clpAPI,numeric-method	addCols-methods
addCols,optObj_cplexAPI,numeric-method	addCols-methods
addCols,optObj_glpkAPI,numeric-method	addCols-methods
addCols,optObj_lpSolveAPI,numeric-method	addCols-methods
addCols-methods	addCols-methods
addColsToProb	addColsToProb-methods
addColsToProb,optObj_clpAPI-method	addColsToProb-methods
addColsToProb,optObj_cplexAPI-method	addColsToProb-methods
addColsToProb,optObj_glpkAPI-method	addColsToProb-methods
addColsToProb,optObj_lpSolveAPI-method	addColsToProb-methods
addColsToProb-methods	addColsToProb-methods
addExchReact	addExchReact
addReact	addReact
addReact,modelorg,ANY-method	addReact
addReact,modelorg-method	addReact
addRows	addRows-methods
addRows,optObj_clpAPI,numeric-method	addRows-methods
addRows,optObj_cplexAPI,numeric-method	addRows-methods
addRows,optObj_glpkAPI,numeric-method	addRows-methods
addRows,optObj_lpSolveAPI,numeric-method	addRows-methods
addRows-methods	addRows-methods
addRowsCols	addRowsCols-methods
addRowsCols,optObj_clpAPI,numeric,numeric-method	addRowsCols-methods
addRowsCols,optObj_cplexAPI,numeric,numeric-method	addRowsCols-methods
addRowsCols,optObj_glpkAPI,numeric,numeric-method	addRowsCols-methods
addRowsCols,optObj_lpSolveAPI,numeric,numeric-method	addRowsCols-methods
addRowsCols-methods	addRowsCols-methods
addRowsToProb	addRowsToProb-methods
addRowsToProb,optObj_clpAPI-method	addRowsToProb-methods
addRowsToProb,optObj_cplexAPI-method	addRowsToProb-methods
addRowsToProb,optObj_glpkAPI-method	addRowsToProb-methods
addRowsToProb,optObj_lpSolveAPI-method	addRowsToProb-methods
addRowsToProb-methods	addRowsToProb-methods
addSolver	addSolver
ALGORITHM	SYBIL_SETTINGS
algorithm	optsol-class
algorithm,optsol-method	optsol-class
algorithm,sysBiolAlg-method	sysBiolAlg-class
algorithm<-	optsol-class
algorithm<-,optsol-method	optsol-class
algorithm<-,sysBiolAlg-method	sysBiolAlg-class
alg_par	sysBiolAlg-class
alg_par,optsol-method	optsol-class
alg_par,sysBiolAlg-method	sysBiolAlg-class
alg_par<-	sysBiolAlg-class
alg_par<-,optsol-method	optsol-class
alg_par<-,sysBiolAlg-method	sysBiolAlg-class
allGenes	modelorg-class
allGenes,modelorg-method	modelorg-class
allGenes<-	modelorg-class
allGenes<-,modelorg-method	modelorg-class
applyChanges	applyChanges-methods
applyChanges,sysBiolAlg-method	applyChanges-methods
applyChanges,sysBiolAlg_room-method	applyChanges-methods
applyChanges-methods	applyChanges-methods
backupProb	backupProb-methods
backupProb,optObj_clpAPI-method	backupProb-methods
backupProb,optObj_cplexAPI-method	backupProb-methods
backupProb,optObj_glpkAPI-method	backupProb-methods
backupProb,optObj_lpSolveAPI-method	backupProb-methods
backupProb-methods	backupProb-methods
blocked	optsol_blockedReact-class
blocked,optsol_blockedReact-method	optsol_blockedReact-class
blocked<-	optsol_blockedReact-class
blocked<-,optsol_blockedReact-method	optsol_blockedReact-class
blockedReact	blockedReact
blReact	optsol_fluxVar-class
blReact,optsol_fluxVar-method	optsol_fluxVar-class
changeBounds	changeBounds
changeColsBnds	changeColsBnds-methods
changeColsBnds,optObj_clpAPI-method	changeColsBnds-methods
changeColsBnds,optObj_cplexAPI-method	changeColsBnds-methods
changeColsBnds,optObj_glpkAPI-method	changeColsBnds-methods
changeColsBnds,optObj_lpSolveAPI-method	changeColsBnds-methods
changeColsBnds-methods	changeColsBnds-methods
changeColsBndsObjCoefs	changeColsBndsObjCoefs-methods
changeColsBndsObjCoefs,optObj_clpAPI-method	changeColsBndsObjCoefs-methods
changeColsBndsObjCoefs,optObj_cplexAPI-method	changeColsBndsObjCoefs-methods
changeColsBndsObjCoefs,optObj_glpkAPI-method	changeColsBndsObjCoefs-methods
changeColsBndsObjCoefs,optObj_lpSolveAPI-method	changeColsBndsObjCoefs-methods
changeColsBndsObjCoefs-methods	changeColsBndsObjCoefs-methods
changeGPR	changeGPR
changeMatrixRow	changeMatrixRow-methods
changeMatrixRow,optObj_cplexAPI-method	changeMatrixRow-methods
changeMatrixRow,optObj_glpkAPI-method	changeMatrixRow-methods
changeMatrixRow,optObj_lpSolveAPI-method	changeMatrixRow-methods
changeMatrixRow-methods	changeMatrixRow-methods
changeMaxObj	sysBiolAlg_mtf-class
changeMaxObj,sysBiolAlg_mtf-method	sysBiolAlg_mtf-class
changeObjCoefs	changeObjCoefs-methods
changeObjCoefs,optObj_clpAPI-method	changeObjCoefs-methods
changeObjCoefs,optObj_cplexAPI-method	changeObjCoefs-methods
changeObjCoefs,optObj_glpkAPI-method	changeObjCoefs-methods
changeObjCoefs,optObj_lpSolveAPI-method	changeObjCoefs-methods
changeObjCoefs-methods	changeObjCoefs-methods
changeObjFunc	changeObjFunc
changeRowsBnds	changeRowsBnds-methods
changeRowsBnds,optObj_clpAPI-method	changeRowsBnds-methods
changeRowsBnds,optObj_cplexAPI-method	changeRowsBnds-methods
changeRowsBnds,optObj_glpkAPI-method	changeRowsBnds-methods
changeRowsBnds,optObj_lpSolveAPI-method	changeRowsBnds-methods
changeRowsBnds-methods	changeRowsBnds-methods
changeUptake	changeUptake-methods
changeUptake,modelorg-method	changeUptake-methods
changeUptake-methods	changeUptake-methods
checkAlgorithm	checkAkgorithm
checkDefaultMethod	checkDefaultMethod
checkOptSol	checkOptSol-methods
checkOptSol,optsol-method	checkOptSol-methods
checkOptSol-methods	checkOptSol-methods
checkReactId	checkReactId
checksol	checksol-class
checksol-class	checksol-class
checkSolStat	optObj-class
checkStat	optsol-class
checkStat,optsol-method	optsol-class
checkVersion	checkVersion-methods
checkVersion,modelorg	checkVersion-methods
checkVersion,modelorg-method	checkVersion-methods
checkVersion-methods	checkVersion-methods
chlb	optsol_fluxdel-class
chlb,optsol_fluxdel-method	optsol_fluxdel-class
chlb<-	optsol_fluxdel-class
chlb<-,optsol_fluxdel-method	optsol_fluxdel-class
chub	optsol_fluxdel-class
chub,optsol_fluxdel-method	optsol_fluxdel-class
chub<-	optsol_fluxdel-class
chub<-,optsol_fluxdel-method	optsol_fluxdel-class
clpPtr-class	optObj-class
cmd	ppProc-class
cmd,ppProc-method	ppProc-class
cmd<-	ppProc-class
cmd<-,ppProc-method	ppProc-class
comp_attr	modelorg-class
comp_attr,modelorg-method	modelorg-class
comp_attr,react-method	modelorg-class
comp_attr<-	modelorg-class
comp_attr<-,modelorg-method	modelorg-class
comp_attr<-,react-method	modelorg-class
cplexPointer-class	optObj-class
cplexPtr-class	optObj-class
ctrlfl	optsol_robAna-class
ctrlfl,optsol_phpp-method	optsol_phpp-class
ctrlfl,optsol_robAna-method	optsol_robAna-class
ctrlfl<-	optsol_robAna-class
ctrlfl<-,optsol_phpp-method	optsol_phpp-class
ctrlfl<-,optsol_robAna-method	optsol_robAna-class
ctrlr	optsol_robAna-class
ctrlr,optsol_robAna-method	optsol_robAna-class
ctrlr<-	optsol_robAna-class
ctrlr<-,optsol_robAna-method	optsol_robAna-class
deadEndMetabolites	deadEndMetabolites-methods
deadEndMetabolites,modelorg-method	deadEndMetabolites-methods
deadEndMetabolites-methods	deadEndMetabolites-methods
deleted	optsol_fluxdel-class
deleted,optsol_fluxdel-method	optsol_fluxdel-class
deleted,optsol_genedel-method	optsol_genedel-class
delProb	delProb-methods
delProb,optObj_clpAPI-method	delProb-methods
delProb,optObj_cplexAPI-method	delProb-methods
delProb,optObj_glpkAPI-method	delProb-methods
delProb,optObj_lpSolveAPI-method	delProb-methods
delProb-methods	delProb-methods
dels	optsol_fluxdel-class
dels,optsol_fluxdel-method	optsol_fluxdel-class
dels<-	optsol_fluxdel-class
dels<-,optsol_fluxdel-method	optsol_fluxdel-class
didFoot	sybilLog-class
didFoot,sybilLog-method	sybilLog-class
didFoot<-	sybilLog-class
didFoot<-,sybilLog-method	sybilLog-class
dim,modelorg-method	modelorg-class
dim,optObj-method	optObj-class
doubleFluxDel	doubleFluxDel
doubleGeneDel	doubleGeneDel
doubleReact	doubleReact
EasyConstraint	sysBiolAlg_fbaEasyConstraint-class
Ec_core	Ec_core
editEnvir	editEnvir
emsg	sybilError-class
emsg,sybilError-method	sybilError-class
emsg<-	sybilError-class
emsg<-,sybilError-method	sybilError-class
enum	sybilError-class
enum,sybilError-method	sybilError-class
enum<-	sybilError-class
enum<-,sybilError-method	sybilError-class
exit_code	checksol-class
exit_code,checksol-method	checksol-class
exit_code<-	checksol-class
exit_code<-,checksol-method	checksol-class
exit_meaning	checksol-class
exit_meaning,checksol-method	checksol-class
exit_meaning<-	checksol-class
exit_meaning<-,checksol-method	checksol-class
exit_num	checksol-class
exit_num,checksol-method	checksol-class
exit_num<-	checksol-class
exit_num<-,checksol-method	checksol-class
ex_met	summaryOptsol-class
ex_met,summaryOptsol-method	summaryOptsol-class
ex_val	summaryOptsol-class
ex_val,summaryOptsol-method	summaryOptsol-class
fba	sysBiolAlg_fba-class
fbaEasyConstraint	sysBiolAlg_fbaEasyConstraint-class
fenc	sybilLog-class
fenc,sybilLog-method	sybilLog-class
fenc<-	sybilLog-class
fenc<-,sybilLog-method	sybilLog-class
fh	sybilLog-class
fh,sybilLog-method	sybilLog-class
fh<-	sybilLog-class
fh<-,sybilLog-method	sybilLog-class
file-class	sybilLog-class
findExchReact	findExchReact
fldind	optsol-class
fldind,optsol-method	optsol-class
fldind,sysBiolAlg-method	sysBiolAlg-class
fldind<-	optsol-class
fldind<-,optsol-method	optsol-class
fldind<-,sysBiolAlg-method	sysBiolAlg-class
fluxdels	optsol_genedel-class
fluxdels,optsol_genedel-method	optsol_genedel-class
fluxdels<-	optsol_genedel-class
fluxdels<-,optsol_genedel-method	optsol_genedel-class
fluxdist	optsol-class
fluxdist,optsol-method	optsol-class
fluxdist<-	optsol-class
fluxdist<-,optsol-method	optsol-class
fluxDistribution	fluxDistribution-class
fluxDistribution-class	fluxDistribution-class
fluxes	optsol-class
fluxes,fluxDistribution-method	fluxDistribution-class
fluxes,optsol-method	optsol-class
fluxes<-	optsol-class
fluxes<-,fluxDistribution-method	fluxDistribution-class
fluxes<-,optsol-method	optsol-class
fluxVar	fluxVar
fname	sybilLog-class
fname,sybilLog-method	sybilLog-class
fname<-	sybilLog-class
fname<-,sybilLog-method	sybilLog-class
fpath	sybilLog-class
fpath,sybilLog-method	sybilLog-class
fpath<-	sybilLog-class
fpath<-,sybilLog-method	sybilLog-class
fv	sysBiolAlg_fv-class
geneDel	geneDel
geneDeletion	geneDeletion
genes	modelorg-class
genes,modelorg-method	modelorg-class
genes,react-method	modelorg-class
genes<-	modelorg-class
genes<-,modelorg-method	modelorg-class
genes<-,react-method	modelorg-class
getColPrim	getColPrim-methods
getColPrim,optObj_clpAPI,numeric-method	getColPrim-methods
getColPrim,optObj_cplexAPI,numeric-method	getColPrim-methods
getColPrim,optObj_glpkAPI,numeric-method	getColPrim-methods
getColPrim,optObj_lpSolveAPI,numeric-method	getColPrim-methods
getColPrim-methods	getColPrim-methods
getColsLowBnds	getColsLowBnds-methods
getColsLowBnds,optObj_clpAPI,numeric-method	getColsLowBnds-methods
getColsLowBnds,optObj_cplexAPI,numeric-method	getColsLowBnds-methods
getColsLowBnds,optObj_glpkAPI,numeric-method	getColsLowBnds-methods
getColsLowBnds,optObj_lpSolveAPI,numeric-method	getColsLowBnds-methods
getColsLowBnds-methods	getColsLowBnds-methods
getColsNames	getColsNames-methods
getColsNames,optObj_cplexAPI,numeric-method	getColsNames-methods
getColsNames,optObj_glpkAPI,numeric-method	getColsNames-methods
getColsNames,optObj_lpSolveAPI,numeric-method	getColsNames-methods
getColsNames-methods	getColsNames-methods
getColsUppBnds	getColsUppBnds-methods
getColsUppBnds,optObj_clpAPI,numeric-method	getColsUppBnds-methods
getColsUppBnds,optObj_cplexAPI,numeric-method	getColsUppBnds-methods
getColsUppBnds,optObj_glpkAPI,numeric-method	getColsUppBnds-methods
getColsUppBnds,optObj_lpSolveAPI,numeric-method	getColsUppBnds-methods
getColsUppBnds-methods	getColsUppBnds-methods
getFluxDist	getFluxDist-methods
getFluxDist,optObj_clpAPI-method	getFluxDist-methods
getFluxDist,optObj_cplexAPI-method	getFluxDist-methods
getFluxDist,optObj_glpkAPI-method	getFluxDist-methods
getFluxDist,optObj_lpSolveAPI-method	getFluxDist-methods
getFluxDist,optsol-method	getFluxDist-methods
getFluxDist-methods	getFluxDist-methods
getMeanReturn	optObj-class
getMeanStatus	optObj-class
getNetFlux	netFlux-class
getNumCols	getNumCols-methods
getNumCols,optObj_clpAPI-method	getNumCols-methods
getNumCols,optObj_cplexAPI-method	getNumCols-methods
getNumCols,optObj_glpkAPI-method	getNumCols-methods
getNumCols,optObj_lpSolveAPI-method	getNumCols-methods
getNumCols-methods	getNumCols-methods
getNumNnz	getNumNnz-methods
getNumNnz,optObj_clpAPI-method	getNumNnz-methods
getNumNnz,optObj_cplexAPI-method	getNumNnz-methods
getNumNnz,optObj_glpkAPI-method	getNumNnz-methods
getNumNnz-methods	getNumNnz-methods
getNumRows	getNumRows-methods
getNumRows,optObj_clpAPI-method	getNumRows-methods
getNumRows,optObj_cplexAPI-method	getNumRows-methods
getNumRows,optObj_glpkAPI-method	getNumRows-methods
getNumRows,optObj_lpSolveAPI-method	getNumRows-methods
getNumRows-methods	getNumRows-methods
getObjCoefs	getObjCoefs-methods
getObjCoefs,optObj_clpAPI,numeric-method	getObjCoefs-methods
getObjCoefs,optObj_cplexAPI,numeric-method	getObjCoefs-methods
getObjCoefs,optObj_glpkAPI,numeric-method	getObjCoefs-methods
getObjCoefs,optObj_lpSolveAPI,numeric-method	getObjCoefs-methods
getObjCoefs-methods	getObjCoefs-methods
getObjDir	getObjDir-methods
getObjDir,optObj_clpAPI-method	getObjDir-methods
getObjDir,optObj_cplexAPI-method	getObjDir-methods
getObjDir,optObj_glpkAPI-method	getObjDir-methods
getObjDir,optObj_lpSolveAPI-method	getObjDir-methods
getObjDir-methods	getObjDir-methods
getObjVal	getObjVal-methods
getObjVal,optObj_clpAPI-method	getObjVal-methods
getObjVal,optObj_cplexAPI-method	getObjVal-methods
getObjVal,optObj_glpkAPI-method	getObjVal-methods
getObjVal,optObj_lpSolveAPI-method	getObjVal-methods
getObjVal-methods	getObjVal-methods
getReaction	mergeReact2Modelorg
getReaction,modelorg,ANY-method	mergeReact2Modelorg
getReaction,modelorg-method	mergeReact2Modelorg
getRedCosts	getRedCosts-methods
getRedCosts,optObj_clpAPI-method	getRedCosts-methods
getRedCosts,optObj_cplexAPI-method	getRedCosts-methods
getRedCosts,optObj_glpkAPI-method	getRedCosts-methods
getRedCosts,optObj_lpSolveAPI-method	getRedCosts-methods
getRedCosts,optsol_phpp-method	optsol_phpp-class
getRedCosts-methods	getRedCosts-methods
getRowsLowBnds	getRowsLowBnds-methods
getRowsLowBnds,optObj_clpAPI,numeric-method	getRowsLowBnds-methods
getRowsLowBnds,optObj_cplexAPI,numeric-method	getRowsLowBnds-methods
getRowsLowBnds,optObj_glpkAPI,numeric-method	getRowsLowBnds-methods
getRowsLowBnds,optObj_lpSolveAPI,numeric-method	getRowsLowBnds-methods
getRowsLowBnds-methods	getRowsLowBnds-methods
getRowsNames	getRowsNames-methods
getRowsNames,optObj_cplexAPI,numeric-method	getRowsNames-methods
getRowsNames,optObj_glpkAPI,numeric-method	getRowsNames-methods
getRowsNames,optObj_lpSolveAPI,numeric-method	getRowsNames-methods
getRowsNames-methods	getRowsNames-methods
getRowsUppBnds	getRowsUppBnds-methods
getRowsUppBnds,optObj_clpAPI,numeric-method	getRowsUppBnds-methods
getRowsUppBnds,optObj_cplexAPI,numeric-method	getRowsUppBnds-methods
getRowsUppBnds,optObj_glpkAPI,numeric-method	getRowsUppBnds-methods
getRowsUppBnds,optObj_lpSolveAPI,numeric-method	getRowsUppBnds-methods
getRowsUppBnds-methods	getRowsUppBnds-methods
getSolStat	getSolStat-methods
getSolStat,optObj_clpAPI-method	getSolStat-methods
getSolStat,optObj_cplexAPI-method	getSolStat-methods
getSolStat,optObj_glpkAPI-method	getSolStat-methods
getSolStat,optObj_lpSolveAPI-method	getSolStat-methods
getSolStat-methods	getSolStat-methods
getSolverParm	getSolverParm-methods
getSolverParm,optObj_clpAPI-method	getSolverParm-methods
getSolverParm,optObj_cplexAPI-method	getSolverParm-methods
getSolverParm,optObj_glpkAPI-method	getSolverParm-methods
getSolverParm,optObj_lpSolveAPI-method	getSolverParm-methods
getSolverParm-methods	getSolverParm-methods
getsybilenv	getsybilenv
glpkPtr-class	optObj-class
gpr	modelorg-class
gpr,modelorg-method	modelorg-class
gpr,react-method	modelorg-class
gpr<-	modelorg-class
gpr<-,modelorg-method	modelorg-class
gpr<-,react-method	modelorg-class
gprRule	modelorg-class
gprRule,react-method	modelorg-class
gprRule<-	modelorg-class
gprRule<-,react-method	modelorg-class
gprRules	modelorg-class
gprRules,modelorg-method	modelorg-class
gprRules<-	modelorg-class
gprRules<-,modelorg-method	modelorg-class
hasEffect	optsol_genedel-class
hasEffect,optsol_genedel-method	optsol_genedel-class
hasEffect<-	optsol_genedel-class
hasEffect<-,optsol_genedel-method	optsol_genedel-class
image,summaryOptsol-method	summaryOptsol-class
ind	ppProc-class
ind,ppProc-method	ppProc-class
ind<-	ppProc-class
ind<-,ppProc-method	ppProc-class
initProb	initProb-methods
initProb,optObj_clpAPI-method	initProb-methods
initProb,optObj_cplexAPI-method	initProb-methods
initProb,optObj_glpkAPI-method	initProb-methods
initProb,optObj_lpSolveAPI-method	initProb-methods
initProb-methods	initProb-methods
irrev	modelorg_irrev-class
irrev,modelorg_irrev-method	modelorg_irrev-class
irrev2rev	modelorg_irrev-class
irrev2rev,modelorg_irrev-method	modelorg_irrev-class
irrev2rev<-	modelorg_irrev-class
irrev2rev<-,modelorg_irrev-method	modelorg_irrev-class
irrev<-	modelorg_irrev-class
irrev<-,modelorg_irrev-method	modelorg_irrev-class
length,netFlux-method	netFlux-class
length,optsol-method	optsol-class
length,reactId-method	reactId-class
lethal	optsol_fluxdel-class
lethal,optsol_fluxdel-method	optsol_fluxdel-class
lmoma	sysBiolAlg_lmoma-class
loadLPprob	loadLPprob-methods
loadLPprob,optObj_clpAPI-method	loadLPprob-methods
loadLPprob,optObj_cplexAPI-method	loadLPprob-methods
loadLPprob,optObj_glpkAPI-method	loadLPprob-methods
loadLPprob,optObj_lpSolveAPI-method	loadLPprob-methods
loadLPprob-methods	loadLPprob-methods
loadMatrixPerColumnLPSOLVE	optObj_lpSolveAPI-class
loadQobj	loadQobj-methods
loadQobj,optObj_cplexAPI,Matrix-method	loadQobj-methods
loadQobj,optObj_cplexAPI,numeric-method	loadQobj-methods
loadQobj-methods	loadQobj-methods
logCall	sybilLog-class
logCall,sybilLog-method	sybilLog-class
logClose<-	sybilLog-class
logClose<-,sybilLog-method	sybilLog-class
logComment	sybilLog-class
logComment,sybilLog-method	sybilLog-class
logError	sybilLog-class
logError,sybilLog,ANY,ANY-method	sybilLog-class
logError,sybilLog,ANY,numeric-method	sybilLog-class
logError,sybilLog-method	sybilLog-class
logFH	sybilLog-class
logFH,sybilLog-method	sybilLog-class
logFileFH	sybilLog-class
logFoot<-	sybilLog-class
logFoot<-,sybilLog-method	sybilLog-class
logHead	sybilLog-class
logHead,sybilLog-method	sybilLog-class
loglevel	sybilLog-class
loglevel,sybilLog-method	sybilLog-class
loglevel<-	sybilLog-class
loglevel<-,sybilLog-method	sybilLog-class
logMessage	sybilLog-class
logMessage,sybilLog-method	sybilLog-class
logOptimization	sybilLog-class
logOptimization,sybilLog-method	sybilLog-class
logOptimizationTH	sybilLog-class
logOptimizationTH,sybilLog-method	sybilLog-class
logStep<-	sybilLog-class
logStep<-,sybilLog-method	sybilLog-class
logWarning	sybilLog-class
logWarning,sybilLog-method	sybilLog-class
lowbnd	modelorg-class
lowbnd,modelorg-method	modelorg-class
lowbnd,react-method	modelorg-class
lowbnd,reactId_Exch-method	reactId_Exch-class
lowbnd<-	modelorg-class
lowbnd<-,modelorg-method	modelorg-class
lowbnd<-,react-method	modelorg-class
lowbnd<-,reactId_Exch-method	reactId_Exch-class
lpExtPtr-class	optObj-class
lp_dir	optsol-class
lp_dir,optsol-method	optsol-class
lp_dir<-	optsol-class
lp_dir<-,optsol,character-method	optsol-class
lp_dir<-,optsol,factor-method	optsol-class
lp_dir<-,optsol,numeric-method	optsol-class
lp_num_cols	optsol-class
lp_num_cols,optsol-method	optsol-class
lp_num_cols<-	optsol-class
lp_num_cols<-,optsol-method	optsol-class
lp_num_rows	optsol-class
lp_num_rows,optsol-method	optsol-class
lp_num_rows<-	optsol-class
lp_num_rows<-,optsol-method	optsol-class
lp_obj	optsol-class
lp_obj,optsol-method	optsol-class
lp_obj<-	optsol-class
lp_obj<-,optsol-method	optsol-class
lp_ok	optsol-class
lp_ok,optsol-method	optsol-class
lp_ok<-	optsol-class
lp_ok<-,optsol-method	optsol-class
lp_stat	optsol-class
lp_stat,optsol-method	optsol-class
lp_stat<-	optsol-class
lp_stat<-,optsol-method	optsol-class
lstname	sybilLog-class
lstname,sybilLog-method	sybilLog-class
makeOptsolMO	makeOptsolMO
matchrev	modelorg_irrev-class
matchrev,modelorg_irrev-method	modelorg_irrev-class
matchrev<-	modelorg_irrev-class
matchrev<-,modelorg_irrev-method	modelorg_irrev-class
MAXIMUM	SYBIL_SETTINGS
maxSol	optsol_blockedReact-class
maxSol,optsol_blockedReact-method	optsol_blockedReact-class
maxSol,optsol_fluxVar-method	optsol_fluxVar-class
mergeReact2Modelorg	mergeReact2Modelorg
METHOD	SYBIL_SETTINGS
method	optsol-class
method,optObj-method	optObj-class
method,optsol-method	optsol-class
method<-	optsol-class
method<-,optsol-method	optsol-class
met_attr	modelorg-class
met_attr,modelorg-method	modelorg-class
met_attr,react-method	modelorg-class
met_attr<-	modelorg-class
met_attr<-,modelorg-method	modelorg-class
met_attr<-,react-method	modelorg-class
met_comp	modelorg-class
met_comp,modelorg-method	modelorg-class
met_comp,react-method	modelorg-class
met_comp<-	modelorg-class
met_comp<-,modelorg-method	modelorg-class
met_comp<-,react-method	modelorg-class
met_de	modelorg-class
met_de,modelorg-method	modelorg-class
met_de<-	modelorg-class
met_de<-,modelorg-method	modelorg-class
met_id	modelorg-class
met_id,modelorg-method	modelorg-class
met_id,react-method	modelorg-class
met_id,reactId_Exch-method	reactId_Exch-class
met_id<-	modelorg-class
met_id<-,modelorg-method	modelorg-class
met_id<-,react-method	modelorg-class
met_id<-,reactId_Exch-method	reactId_Exch-class
met_name	modelorg-class
met_name,modelorg-method	modelorg-class
met_name,react-method	modelorg-class
met_name<-	modelorg-class
met_name<-,modelorg-method	modelorg-class
met_name<-,react-method	modelorg-class
met_num	modelorg-class
met_num,modelorg-method	modelorg-class
met_num<-	modelorg-class
met_num<-,modelorg-method	modelorg-class
met_pos	reactId_Exch-class
met_pos,reactId_Exch-method	reactId_Exch-class
met_pos<-	reactId_Exch-class
met_pos<-,reactId_Exch-method	reactId_Exch-class
met_single	modelorg-class
met_single,modelorg-method	modelorg-class
met_single<-	modelorg-class
met_single<-,modelorg-method	modelorg-class
minSol	optsol_blockedReact-class
minSol,optsol_blockedReact-method	optsol_blockedReact-class
minSol,optsol_fluxVar-method	optsol_fluxVar-class
mod2irrev	mod2irrev
modelorg	modelorg-class
modelorg-class	modelorg-class
modelorg2ExPA	modelorg2ExPA
modelorg2text	sybil-internal
modelorg2tsv	modelorg2tsv
modelorg_irrev	modelorg_irrev-class
modelorg_irrev-class	modelorg_irrev-class
mod_attr	modelorg-class
mod_attr,modelorg-method	modelorg-class
mod_attr,react-method	modelorg-class
mod_attr<-	modelorg-class
mod_attr<-,modelorg-method	modelorg-class
mod_attr<-,react-method	modelorg-class
mod_compart	modelorg-class
mod_compart,modelorg-method	modelorg-class
mod_compart<-	modelorg-class
mod_compart<-,modelorg-method	modelorg-class
mod_desc	modelorg-class
mod_desc,modelorg-method	modelorg-class
mod_desc<-	modelorg-class
mod_desc<-,modelorg-method	modelorg-class
mod_id	modelorg-class
mod_id,modelorg-method	modelorg-class
mod_id,optsol-method	optsol-class
mod_id,reactId-method	reactId-class
mod_id,summaryOptsol-method	summaryOptsol-class
mod_id<-	modelorg-class
mod_id<-,modelorg-method	modelorg-class
mod_id<-,optsol-method	optsol-class
mod_id<-,reactId-method	reactId-class
mod_id<-,summaryOptsol-method	summaryOptsol-class
mod_key	modelorg-class
mod_key,modelorg-method	modelorg-class
mod_key,optsol-method	optsol-class
mod_key,reactId-method	reactId-class
mod_key,summaryOptsol-method	summaryOptsol-class
mod_key<-	modelorg-class
mod_key<-,modelorg-method	modelorg-class
mod_key<-,optsol-method	optsol-class
mod_key<-,reactId-method	reactId-class
mod_key<-,summaryOptsol-method	summaryOptsol-class
mod_name	modelorg-class
mod_name,modelorg-method	modelorg-class
mod_name<-	modelorg-class
mod_name<-,modelorg-method	modelorg-class
mod_obj	optsol-class
mod_obj,optsol-method	optsol-class
mod_obj,summaryOptsol-method	summaryOptsol-class
mod_obj<-	summaryOptsol-class
mod_obj<-,summaryOptsol-method	summaryOptsol-class
moma	sysBiolAlg_moma-class
mtf	sysBiolAlg_mtf-class
mtfEasyConstraint	sysBiolAlg_fbaEasyConstraint-class
multiDel	multiDel
nc	sysBiolAlg-class
nc,sysBiolAlg-method	sysBiolAlg-class
nc<-	sysBiolAlg-class
nc<-,sysBiolAlg-method	sysBiolAlg-class
netFlux	netFlux-class
netFlux-class	netFlux-class
nfluxes	optsol-class
nfluxes,optsol-method	optsol-class
nnzero,fluxDistribution-method	fluxDistribution-class
nnzero,summaryOptsol-method	summaryOptsol-class
nr	sysBiolAlg-class
nr,sysBiolAlg-method	sysBiolAlg-class
nr<-	sysBiolAlg-class
nr<-,sysBiolAlg-method	sysBiolAlg-class
num_of_fluxes	fluxDistribution-class
num_of_fluxes,fluxDistribution-method	fluxDistribution-class
num_of_prob	optsol-class
num_of_prob,checksol-method	checksol-class
num_of_prob,optsol-method	optsol-class
num_of_prob<-	optsol-class
num_of_prob<-,checksol-method	checksol-class
num_of_prob<-,optsol-method	optsol-class
nvar	fluxDistribution-class
nvar,fluxDistribution-method	fluxDistribution-class
nzeros	summaryOptsol-class
nzeros,summaryOptsol-method	summaryOptsol-class
object	sybil-internal
obj_coef	modelorg-class
obj_coef,modelorg-method	modelorg-class
obj_coef,optsol-method	optsol-class
obj_coef,react-method	modelorg-class
obj_coef<-	modelorg-class
obj_coef<-,modelorg-method	modelorg-class
obj_coef<-,optsol-method	optsol-class
obj_coef<-,react-method	modelorg-class
obj_func	optsol-class
obj_func,optsol-method	optsol-class
obj_func<-	optsol-class
obj_func<-,optsol-method	optsol-class
oneFluxDel	oneFluxDel
oneGeneDel	oneGeneDel
onlyChangeGPR	onlyChangeGPR
onlyCheckGPR	onlyCheckGPR
optimizeProb	optimizeProb-methods
optimizeProb,modelorg-method	optimizeProb-methods
optimizeProb,sysBiolAlg-method	optimizeProb-methods
optimizeProb-methods	optimizeProb-methods
optimizer	optimizer
optObj	optObj
optObj-class	optObj-class
optObj_clpAPI-class	optObj_clpAPI-class
optObj_cplexAPI-class	optObj_cplexAPI-class
optObj_glpkAPI-class	optObj_glpkAPI-class
optObj_lpSolveAPI-class	optObj_lpSolveAPI-class
optsol	optsol-class
optsol-class	optsol-class
optsol_blockedReact-class	optsol_blockedReact-class
optsol_fluxdel-class	optsol_fluxdel-class
optsol_fluxVar-class	optsol_fluxVar-class
optsol_genedel-class	optsol_genedel-class
optsol_optimizeProb-class	optsol_optimizeProb-class
optsol_phpp-class	optsol_phpp-class
optsol_robAna-class	optsol_robAna-class
OPT_DIRECTION	SYBIL_SETTINGS
pa	ppProc-class
pa,ppProc-method	ppProc-class
pa<-	ppProc-class
pa<-,ppProc-method	ppProc-class
PATH_TO_MODEL	SYBIL_SETTINGS
phpp	phpp
plot,fluxDistribution,missing-method	fluxDistribution-class
plot,optsol,missing-method	optsol-class
plot,optsol_fluxVar,missing-method	optsol_fluxVar-class
plot,optsol_phpp,character-method	optsol_phpp-class
plot,optsol_phpp,missing-method	optsol_phpp-class
plot,optsol_robAna,missing-method	optsol_robAna-class
plot,summaryOptsol,missing-method	summaryOptsol-class
plotRangeVar	optsol_fluxVar-class
plotRangeVar,optsol_fluxVar-method	optsol_fluxVar-class
pointerToProb	optObj-class
pointerToProb-class	optObj-class
postProc	optsol_optimizeProb-class
postProc,optsol_optimizeProb-method	optsol_optimizeProb-class
postProc<-	optsol_optimizeProb-class
postProc<-,optsol_optimizeProb-method	optsol_optimizeProb-class
ppProc	ppProc-class
ppProc-class	ppProc-class
preProc	optsol_optimizeProb-class
preProc,optsol_optimizeProb-method	optsol_optimizeProb-class
preProc<-	optsol_optimizeProb-class
preProc<-,optsol_optimizeProb-method	optsol_optimizeProb-class
printExchange	summaryOptsol-class
printExchange,summaryOptsol-method	summaryOptsol-class
printMetabolite	printMetabolite-methods
printMetabolite,modelorg-method	printMetabolite-methods
printMetabolite-methods	printMetabolite-methods
printObjFunc	modelorg-class
printObjFunc,modelorg-method	modelorg-class
printReaction	printReaction-methods
printReaction,modelorg,ANY-method	printReaction-methods
printReaction,react,ANY-method	printReaction-methods
printReaction,summaryOptsol,modelorg-method	printReaction-methods
printReaction-methods	printReaction-methods
problem	sysBiolAlg-class
problem,sysBiolAlg-method	sysBiolAlg-class
probType	optObj-class
probType,optObj-method	optObj-class
promptSysBiolAlg	promptSysBiolAlg
rate	netFlux-class
rate,netFlux-method	netFlux-class
react	modelorg-class
react,optsol_blockedReact-method	optsol_blockedReact-class
react,optsol_fluxVar-method	optsol_fluxVar-class
react-class	modelorg-class
react<-	optsol_blockedReact-class
react<-,optsol_blockedReact-method	optsol_blockedReact-class
react<-,optsol_fluxVar-method	optsol_fluxVar-class
reactId	reactId-class
reactId-class	reactId-class
reactId_Exch	reactId_Exch-class
reactId_Exch-class	reactId_Exch-class
react_attr	modelorg-class
react_attr,modelorg-method	modelorg-class
react_attr,react-method	modelorg-class
react_attr<-	modelorg-class
react_attr<-,modelorg-method	modelorg-class
react_attr<-,react-method	modelorg-class
react_de	modelorg-class
react_de,modelorg-method	modelorg-class
react_de,react-method	modelorg-class
react_de<-	modelorg-class
react_de<-,modelorg-method	modelorg-class
react_de<-,react-method	modelorg-class
react_id	modelorg-class
react_id,modelorg-method	modelorg-class
react_id,netFlux-method	netFlux-class
react_id,optsol-method	optsol-class
react_id,react-method	modelorg-class
react_id,reactId-method	reactId-class
react_id<-	modelorg-class
react_id<-,modelorg-method	modelorg-class
react_id<-,netFlux-method	netFlux-class
react_id<-,optsol-method	optsol-class
react_id<-,react-method	modelorg-class
react_id<-,reactId-method	reactId-class
react_name	modelorg-class
react_name,modelorg-method	modelorg-class
react_name,react-method	modelorg-class
react_name<-	modelorg-class
react_name<-,modelorg-method	modelorg-class
react_name<-,react-method	modelorg-class
react_num	modelorg-class
react_num,modelorg-method	modelorg-class
react_num<-	modelorg-class
react_num<-,modelorg-method	modelorg-class
react_pos	reactId-class
react_pos,reactId-method	reactId-class
react_pos<-	reactId-class
react_pos<-,reactId-method	reactId-class
react_rev	modelorg-class
react_rev,modelorg-method	modelorg-class
react_rev,react-method	modelorg-class
react_rev<-	modelorg-class
react_rev<-,modelorg-method	modelorg-class
react_rev<-,react-method	modelorg-class
react_single	modelorg-class
react_single,modelorg-method	modelorg-class
react_single,react-method	modelorg-class
react_single<-	modelorg-class
react_single<-,modelorg-method	modelorg-class
react_single<-,react-method	modelorg-class
readProb	readProb-methods
readProb,optObj_clpAPI,character-method	readProb-methods
readProb,optObj_cplexAPI,character-method	readProb-methods
readProb,optObj_glpkAPI,character-method	readProb-methods
readProb,optObj_lpSolveAPI,character-method	readProb-methods
readProb-methods	readProb-methods
readTEXTmod	sybil-internal
readTSVmod	readTSVmod
resetChanges	resetChanges-methods
resetChanges,sysBiolAlg-method	resetChanges-methods
resetChanges,sysBiolAlg_room-method	resetChanges-methods
resetChanges-methods	resetChanges-methods
return_codeLPSOLVE	optObj_lpSolveAPI-class
rev2irrev	modelorg_irrev-class
rev2irrev,modelorg_irrev-method	modelorg_irrev-class
rev2irrev<-	modelorg_irrev-class
rev2irrev<-,modelorg_irrev-method	modelorg_irrev-class
rmReact	rmReact
robAna	robAna
room	sysBiolAlg_room-class
rxnGeneMat	modelorg-class
rxnGeneMat,modelorg-method	modelorg-class
rxnGeneMat<-	modelorg-class
rxnGeneMat<-,modelorg-method	modelorg-class
S	modelorg-class
s	modelorg-class
S,modelorg-method	modelorg-class
s,react-method	modelorg-class
S<-	modelorg-class
s<-	modelorg-class
S<-,modelorg-method	modelorg-class
s<-,react-method	modelorg-class
scaleProb	scaleProb-methods
scaleProb,optObj_clpAPI-method	scaleProb-methods
scaleProb,optObj_cplexAPI-method	scaleProb-methods
scaleProb,optObj_glpkAPI-method	scaleProb-methods
scaleProb,optObj_lpSolveAPI-method	scaleProb-methods
scaleProb-methods	scaleProb-methods
sensitivityAnalysis	sensitivityAnalysis-methods
sensitivityAnalysis,optObj_cplexAPI-method	sensitivityAnalysis-methods
sensitivityAnalysis,optObj_glpkAPI-method	sensitivityAnalysis-methods
sensitivityAnalysis-methods	sensitivityAnalysis-methods
setColsNames	setColsNames-methods
setColsNames,optObj_clpAPI,numeric,character-method	setColsNames-methods
setColsNames,optObj_cplexAPI,numeric,character-method	setColsNames-methods
setColsNames,optObj_glpkAPI,numeric,character-method	setColsNames-methods
setColsNames,optObj_lpSolveAPI,numeric,character-method	setColsNames-methods
setColsNames-methods	setColsNames-methods
setObjDir	setObjDir-methods
setObjDir,optObj_clpAPI,character-method	setObjDir-methods
setObjDir,optObj_clpAPI,numeric-method	setObjDir-methods
setObjDir,optObj_cplexAPI,character-method	setObjDir-methods
setObjDir,optObj_cplexAPI,integer-method	setObjDir-methods
setObjDir,optObj_cplexAPI,numeric-method	setObjDir-methods
setObjDir,optObj_glpkAPI,character-method	setObjDir-methods
setObjDir,optObj_glpkAPI,integer-method	setObjDir-methods
setObjDir,optObj_glpkAPI,numeric-method	setObjDir-methods
setObjDir,optObj_lpSolveAPI,character-method	setObjDir-methods
setObjDir,optObj_lpSolveAPI,numeric-method	setObjDir-methods
setObjDir-methods	setObjDir-methods
setRhsZero	setRhsZero-methods
setRhsZero,optObj_clpAPI-method	setRhsZero-methods
setRhsZero,optObj_cplexAPI-method	setRhsZero-methods
setRhsZero,optObj_glpkAPI-method	setRhsZero-methods
setRhsZero,optObj_lpSolveAPI-method	setRhsZero-methods
setRhsZero-methods	setRhsZero-methods
setRowsNames	setRowsNames-methods
setRowsNames,optObj_clpAPI,numeric,character-method	setRowsNames-methods
setRowsNames,optObj_cplexAPI,numeric,character-method	setRowsNames-methods
setRowsNames,optObj_glpkAPI,numeric,character-method	setRowsNames-methods
setRowsNames,optObj_lpSolveAPI,numeric,character-method	setRowsNames-methods
setRowsNames-methods	setRowsNames-methods
setSolverParm	setSolverParm-methods
setSolverParm,optObj_clpAPI-method	setSolverParm-methods
setSolverParm,optObj_cplexAPI-method	setSolverParm-methods
setSolverParm,optObj_glpkAPI-method	setSolverParm-methods
setSolverParm,optObj_lpSolveAPI-method	setSolverParm-methods
setSolverParm-methods	setSolverParm-methods
show,checksol-method	checksol-class
show,modelorg-method	modelorg-class
show,optsol-method	optsol-class
shrinkMatrix	shrinkMatrix-methods
shrinkMatrix,modelorg-method	shrinkMatrix-methods
shrinkMatrix-methods	shrinkMatrix-methods
singletonMetabolites	singletonMetabolites-methods
singletonMetabolites,modelorg-method	singletonMetabolites-methods
singletonMetabolites-methods	singletonMetabolites-methods
Snnz	modelorg-class
Snnz,modelorg-method	modelorg-class
solveLp	solveLp-methods
solveLp,optObj_clpAPI-method	solveLp-methods
solveLp,optObj_cplexAPI-method	solveLp-methods
solveLp,optObj_glpkAPI-method	solveLp-methods
solveLp,optObj_lpSolveAPI-method	solveLp-methods
solveLp-methods	solveLp-methods
SOLVER	SYBIL_SETTINGS
solver	optsol-class
solver,optObj-method	optObj-class
solver,optsol-method	optsol-class
solver<-	optsol-class
solver<-,optsol-method	optsol-class
SOLVER_CTRL_PARM	SYBIL_SETTINGS
status_code	checksol-class
status_code,checksol-method	checksol-class
status_code<-	checksol-class
status_code<-,checksol-method	checksol-class
status_meaning	checksol-class
status_meaning,checksol-method	checksol-class
status_meaning<-	checksol-class
status_meaning<-,checksol-method	checksol-class
status_num	checksol-class
status_num,checksol-method	checksol-class
status_num<-	checksol-class
status_num<-,checksol-method	checksol-class
stclear	sybilStack
stexists	sybilStack
stfirst	sybilStack
stinit	sybilStack
stlength	sybilStack
stlist	sybilStack
stpop	sybilStack
stpush	sybilStack
stseek	sybilStack
stshift	sybilStack
stunshift	sybilStack
subSys	modelorg-class
subSys,modelorg-method	modelorg-class
subSys,react-method	modelorg-class
subSys<-	modelorg-class
subSys<-,modelorg-method	modelorg-class
subSys<-,react-method	modelorg-class
summaryOptsol	summaryOptsol
summaryOptsol-class	summaryOptsol-class
sybil	sybil-package
sybil-deprecated	deprecated
sybilError	sybilError-class
sybilError-class	sybilError-class
sybilLog	sybilLog-class
sybilLog-class	sybilLog-class
sybilStack	sybilStack
SYBIL_SETTINGS	SYBIL_SETTINGS
sysBiolAlg	sysBiolAlg
sysBiolAlg-class	sysBiolAlg-class
sysBiolAlg_fba	sysBiolAlg_fba-class
sysBiolAlg_fba-class	sysBiolAlg_fba-class
sysBiolAlg_fbaEasyConstraint	sysBiolAlg_fbaEasyConstraint-class
sysBiolAlg_fbaEasyConstraint-class	sysBiolAlg_fbaEasyConstraint-class
sysBiolAlg_fv	sysBiolAlg_fv-class
sysBiolAlg_fv-class	sysBiolAlg_fv-class
sysBiolAlg_lmoma	sysBiolAlg_lmoma-class
sysBiolAlg_lmoma-class	sysBiolAlg_lmoma-class
sysBiolAlg_moma	sysBiolAlg_moma-class
sysBiolAlg_moma-class	sysBiolAlg_moma-class
sysBiolAlg_mtf	sysBiolAlg_mtf-class
sysBiolAlg_mtf-class	sysBiolAlg_mtf-class
sysBiolAlg_mtfEasyConstraint	sysBiolAlg_fbaEasyConstraint-class
sysBiolAlg_mtfEasyConstraint-class	sysBiolAlg_fbaEasyConstraint-class
sysBiolAlg_room	sysBiolAlg_room-class
sysBiolAlg_room-class	sysBiolAlg_room-class
TOLERANCE	SYBIL_SETTINGS
upgradeModelorg	upgradeModelorg
uppbnd	modelorg-class
uppbnd,modelorg-method	modelorg-class
uppbnd,react-method	modelorg-class
uppbnd,reactId_Exch-method	reactId_Exch-class
uppbnd<-	modelorg-class
uppbnd<-,modelorg-method	modelorg-class
uppbnd<-,react-method	modelorg-class
uppbnd<-,reactId_Exch-method	reactId_Exch-class
uptake	reactId_Exch-class
uptake,reactId_Exch-method	reactId_Exch-class
uptake<-	reactId_Exch-class
uptake<-,reactId_Exch-method	reactId_Exch-class
uptMet	reactId_Exch-class
uptMet,reactId_Exch-method	reactId_Exch-class
uptReact	reactId_Exch-class
uptReact,reactId_Exch-method	reactId_Exch-class
USE_NAMES	SYBIL_SETTINGS
verblevel	sybilLog-class
verblevel,sybilLog-method	sybilLog-class
verblevel<-	sybilLog-class
verblevel<-,sybilLog-method	sybilLog-class
version	modelorg-class
version,modelorg-method	modelorg-class
version<-	modelorg-class
version<-,modelorg-method	modelorg-class
writeProb	writeProb-methods
writeProb,optObj_clpAPI,character-method	writeProb-methods
writeProb,optObj_cplexAPI,character-method	writeProb-methods
writeProb,optObj_glpkAPI,character-method	writeProb-methods
writeProb,optObj_lpSolveAPI,character-method	writeProb-methods
writeProb-methods	writeProb-methods
wrong_solver_msg	optObj-class
wrong_type_msg	optObj-class
ypd	ypd
[,fluxDistribution,ANY,ANY,ANY-method	fluxDistribution-class
[,optsol_fluxdel,ANY,ANY,ANY-method	optsol_fluxdel-class
[,reactId,ANY,ANY,ANY-method	reactId-class
[,reactId_Exch,ANY,ANY,ANY-method	reactId_Exch-class
