Index

A

add() (pysces.PyscesPlot2.FIFOBuffer method) addFormula() (pysces.PyscesModel.Function method) addModData() (pysces.PyscesModel.ScanDataObj method) addPoint() (pysces.PyscesModel.ScanDataObj method) addScanParameter() (pysces.PyscesScan.Scanner method) addUserOutput() (pysces.PyscesScan.Scanner method) ALL_VALID (pysces.PyscesModel.ScanDataObj attribute) analyseData() (pysces.PyscesScan.PITCONScanUtils method) AnalyseK() (pysces.PyscesStoich.Stoich method) AnalyseL() (pysces.PyscesStoich.Stoich method)

Analyze() (pysces.PyscesScan.Scanner method) argsl (pysces.PyscesModel.Function attribute) array (pysces.PyscesStoich.StructMatrix attribute) array_kind (pysces.PyscesStoich.MathArrayFunc attribute) array_precision (pysces.PyscesStoich.MathArrayFunc attribute) array_type (pysces.PyscesStoich.MathArrayFunc attribute) assertRank2() (pysces.PyscesStoich.MathArrayFunc method) assignments (pysces.PyscesModel.Event attribute) axisInputStringToList() (pysces.PyscesPlot2.PlotBase method)

B

BackSubstitution() (pysces.PyscesStoich.Stoich method)

BagOfStuff (class in pysces.PyscesModel)

C

castCopyAndTranspose() (pysces.PyscesStoich.MathArrayFunc method) chkmdir() (in module pysces.PyscesModel) chkpsc() (in module pysces.PyscesModel) cidx (pysces.PyscesStoich.StructMatrix attribute) CleanNaNsFromArray() (pysces.PyscesModel.PysMod method) clone() (pysces.PyscesModel.PysMod method) closeAll() (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PyscesUPI method) closeScan() (pysces.PyscesModel.ScanDataObj method) code_string (pysces.PyscesModel.Event attribute) (pysces.PyscesModel.EventAssignment attribute) (pysces.PyscesModel.Function attribute) (pysces.PyscesModel.PieceWise attribute) (pysces.PyscesModel.ReactionObj attribute) col (pysces.PyscesModel.BagOfStuff attribute) (pysces.PyscesStoich.StructMatrix attribute) CommonStyleDefs (pysces.PyscesPlot2.GnuPlotUPI attribute) (pysces.PyscesPlot2.MatplotlibUPI attribute) (pysces.PyscesPlot2.PlotBase attribute) commonType() (pysces.PyscesStoich.MathArrayFunc method) compartment (pysces.PyscesModel.ReactionObj attribute) ConvertFileD2U() (in module pysces.PyscesUtils)

ConvertFileU2D() (in module pysces.PyscesUtils) convertSBML2PSC() (pysces.PyscesInterfaces.Core2interfaces method) CopyModels() (in module pysces.PyscesUtils) CopyTestModels() (in module pysces.PyscesUtils) core (pysces.PyscesInterfaces.Core2interfaces attribute) Core2interfaces (class in pysces.PyscesInterfaces) core2psc (pysces.PyscesInterfaces.Core2interfaces attribute) core2sbml (pysces.PyscesInterfaces.Core2interfaces attribute) CVODE() (pysces.PyscesModel.PysMod method) CVODE_continue() (pysces.PyscesModel.PysMod method) CVODE_continuous_result (pysces.PyscesModel.PysMod attribute) CVODE_EVENTS() (pysces.PyscesModel.PysMod method) CVODE_VPYTHON() (pysces.PyscesModel.PysMod method)

D

DATF_FORMAT (pysces.PyscesPlot2.GnuPlotUPI attribute) DEBUGLEVEL (pysces.PyscesLink.SBWLayoutWebLink attribute) DEBUGMODE (pysces.PyscesLink.SBWLayoutWebLink attribute) delay (pysces.PyscesModel.Event attribute) doEigen() (pysces.PyscesModel.PysMod method) doEigenMca() (pysces.PyscesModel.PysMod method) doEigenShow() (pysces.PyscesModel.PysMod method) doElas() (pysces.PyscesModel.PysMod method) doEModes() (pysces.PyscesLink.METATOOLlink method) doLoad() (pysces.PyscesModel.PysMod method) doMca() (pysces.PyscesModel.PysMod method)

doMcaRC() (pysces.PyscesModel.PysMod method) doMcaRCT() (pysces.PyscesModel.PysMod method) doSim() (pysces.PyscesModel.PysMod method) doSimPerturb() (pysces.PyscesModel.PysMod method) doSimPlot() (pysces.PyscesModel.PysMod method) doState() (pysces.PyscesModel.PysMod method) doStateShow() (pysces.PyscesModel.PysMod method) drawNetworkGetSBMLwithLayout() (pysces.PyscesLink.SBWLayoutWebLink method) DRAWNETWORKLOADED (pysces.PyscesLink.SBWLayoutWebLink attribute) drawNetworkLoadSBML() (pysces.PyscesLink.SBWLayoutWebLink method)

E

EvalCC() (pysces.PyscesModel.PysMod method) EvalEigen() (pysces.PyscesModel.PysMod method) EvalEpar() (pysces.PyscesModel.PysMod method) EvalEvar() (pysces.PyscesModel.PysMod method) EvalRC() (pysces.PyscesModel.PysMod method) EvalRCT() (pysces.PyscesModel.PysMod method) evaluateAssignment() (pysces.PyscesModel.EventAssignment method) Event (class in pysces.PyscesModel) EventAssignment (class in pysces.PyscesModel) export() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method)

exportArray2CSV() (pysces.PyscesUtils.WriteOutput method) exportArray2TXT() (pysces.PyscesUtils.WriteOutput method) exportLabelledArray() (pysces.PyscesUtils.WriteOutput method) exportLabelledArray2CSV() (pysces.PyscesUtils.WriteOutput method) exportLabelledArray2TXT() (pysces.PyscesUtils.WriteOutput method) exportLabelledArrayWithHeader() (pysces.PyscesUtils.WriteOutput method) exportLabelledArrayWithHeader2CSV() (pysces.PyscesUtils.WriteOutput method) exportLabelledArrayWithHeader2TXT() (pysces.PyscesUtils.WriteOutput method) exportLabelledLinkedList() (pysces.PyscesUtils.WriteOutput method) exportSimAsSedML() (pysces.PyscesModel.PysMod method)

F

FIFOBuffer (class in pysces.PyscesPlot2) FINTSLV() (pysces.PyscesModel.PysMod method) Fix_S_fullinput() (pysces.PyscesModel.PysMod method) Fix_S_indinput() (pysces.PyscesModel.PysMod method) Fix_Sim() (pysces.PyscesModel.PysMod method) flux_labels (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute)

fluxes (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute) FluxGenSim() (pysces.PyscesModel.PysMod method) Forcing_Function() (pysces.PyscesModel.PysMod method) formula (pysces.PyscesModel.Event attribute) (pysces.PyscesModel.EventAssignment attribute) (pysces.PyscesModel.Function attribute) (pysces.PyscesModel.PieceWise attribute) (pysces.PyscesModel.ReactionObj attribute) Function (class in pysces.PyscesModel) functions (pysces.PyscesModel.Function attribute)

G

g (pysces.PyscesPlot2.PyscesUPI attribute) g_file_write_array() (pysces.PyscesPlot2.GnuPlotUPI method) g_file_write_array3D() (pysces.PyscesPlot2.GnuPlotUPI method) g_pause() (pysces.PyscesPlot2.GnuPlotUPI method) g_write() (pysces.PyscesPlot2.GnuPlotUPI method) genOn (pysces.PyscesScan.Scanner attribute) get() (pysces.PyscesModel.BagOfStuff method) (pysces.PyscesModel.NewCoreBase method) (pysces.PyscesPlot2.FIFOBuffer method) getAllScanData() (pysces.PyscesModel.ScanDataObj method) getAllSimData() (pysces.PyscesModel.IntegrationDataObj method) getAllStateData() (pysces.PyscesModel.StateDataObj method) getArrayListAsArray() (pysces.PyscesScan.PITCONScanUtils method) getByIdx() (pysces.PyscesStoich.StructMatrix method) getByName() (pysces.PyscesStoich.StructMatrix method) getColsByIdx() (pysces.PyscesStoich.StructMatrix method) getColsByName() (pysces.PyscesStoich.StructMatrix method) getDataAtTime() (pysces.PyscesModel.IntegrationDataObj method) getDataInTimeInterval() (pysces.PyscesModel.IntegrationDataObj method) getEModes() (pysces.PyscesLink.METATOOLlink method) getFluxes() (pysces.PyscesModel.ScanDataObj method) (pysces.PyscesModel.StateDataObj method) getIndexes() (pysces.PyscesStoich.StructMatrix method) getLabels() (pysces.PyscesStoich.StructMatrix method) getModData() (pysces.PyscesModel.ScanDataObj method)

getName() (pysces.PyscesModel.NewCoreBase method) getOutput() (pysces.PyscesModel.IntegrationDataObj method) (pysces.PyscesScan.Scanner method) getRates() (pysces.PyscesModel.IntegrationDataObj method) getResultMatrix() (pysces.PyscesScan.Scanner method) getRowsByIdx() (pysces.PyscesStoich.StructMatrix method) getRowsByName() (pysces.PyscesStoich.StructMatrix method) getRules() (pysces.PyscesModel.IntegrationDataObj method) (pysces.PyscesModel.ScanDataObj method) (pysces.PyscesModel.StateDataObj method) getSBML() (pysces.PyscesLink.SBWLayoutWebLink method) getSBMLlayout() (pysces.PyscesLink.SBWLayoutWebLink method) getScanData() (pysces.PyscesModel.ScanDataObj method) getSimData() (pysces.PyscesModel.IntegrationDataObj method) getSpecies() (pysces.PyscesModel.IntegrationDataObj method) (pysces.PyscesModel.ScanDataObj method) (pysces.PyscesModel.StateDataObj method) getStateData() (pysces.PyscesModel.StateDataObj method) getSVG() (pysces.PyscesLink.SBWLayoutWebLink method) getTime() (pysces.PyscesModel.IntegrationDataObj method) GetUpperMatrix() (pysces.PyscesStoich.Stoich method) GetUpperMatrixUsingQR() (pysces.PyscesStoich.Stoich method) getValue() (pysces.PyscesModel.NumberBase method) getVersion() (pysces.PyscesLink.SBWLayoutWebLink method) getXData() (pysces.PyscesModel.IntegrationDataObj method) (pysces.PyscesModel.ScanDataObj method) (pysces.PyscesModel.StateDataObj method) GnuPlotUPI (class in pysces.PyscesPlot2)

H

HAS_FLUXES (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute) HAS_MOD_DATA (pysces.PyscesModel.ScanDataObj attribute) HAS_RATES (pysces.PyscesModel.IntegrationDataObj attribute) HAS_RULES (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute) HAS_SET_LABELS (pysces.PyscesModel.ScanDataObj attribute) HAS_SPECIES (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute)

HAS_STATE_OUTPUT (pysces.PyscesScan.Scanner attribute) HAS_TIME (pysces.PyscesModel.IntegrationDataObj attribute) HAS_USER_OUTPUT (pysces.PyscesScan.Scanner attribute) HAS_XDATA (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute) hold() (pysces.PyscesPlot2.MatplotlibUPI method) HYBRD() (pysces.PyscesModel.PysMod method)

I

info_moiety_conserve (pysces.PyscesStoich.Stoich attribute) InitialiseCompartments() (pysces.PyscesModel.PysMod method) InitialiseConservationArrays() (pysces.PyscesModel.PysMod method) InitialiseEvents() (pysces.PyscesModel.PysMod method) InitialiseFunctions() (pysces.PyscesModel.PysMod method) InitialiseInputFile() (pysces.PyscesModel.PysMod method) InitialiseModel() (pysces.PyscesModel.PysMod method) InitialiseOldFunctions() (pysces.PyscesModel.PysMod method)

InitialiseRuleChecks() (pysces.PyscesModel.PysMod method) InitialiseRules() (pysces.PyscesModel.PysMod method) IntegrationDataObj (class in pysces.PyscesModel) invalid_state_list (pysces.PyscesScan.Scanner attribute) invalid_state_list_idx (pysces.PyscesScan.Scanner attribute) invalid_states (pysces.PyscesModel.ScanDataObj attribute) IS_VALID (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.StateDataObj attribute)

K

K_split_R() (pysces.PyscesStoich.Stoich method)

L

L_split_R() (pysces.PyscesStoich.Stoich method) layoutModuleGetSVG() (pysces.PyscesLink.SBWLayoutWebLink method) LAYOUTMODULELOADED (pysces.PyscesLink.SBWLayoutWebLink attribute) layoutModuleLoadSBML() (pysces.PyscesLink.SBWLayoutWebLink method) LinAlgError (pysces.PyscesStoich.MathArrayFunc attribute) list() (pysces.PyscesModel.BagOfStuff method) listAllOrdered() (pysces.PyscesModel.BagOfStuff method)

load() (pysces.PyscesModel.BagOfStuff method) LoadFromFile() (pysces.PyscesModel.PysMod method) LoadFromString() (pysces.PyscesModel.PysMod method) loadSBMLFileFromDisk() (pysces.PyscesLink.SBWLayoutWebLink method) loadSBMLFromString() (pysces.PyscesLink.SBWLayoutWebLink method) LSODA() (pysces.PyscesModel.PysMod method)

M

m (pysces.PyscesPlot2.PyscesUPI attribute) makeRange() (pysces.PyscesScan.Scanner method) MathArrayFunc (class in pysces.PyscesStoich) MatplotlibUPI (class in pysces.PyscesPlot2) matrix (pysces.PyscesModel.BagOfStuff attribute) MatrixFloatFix() (pysces.PyscesStoich.MathArrayFunc method) MatrixValueCompare() (pysces.PyscesStoich.MathArrayFunc method) MAX_OPEN_WINDOWS (pysces.PyscesPlot2.MatplotlibUPI attribute) METATOOLlink (class in pysces.PyscesLink)

mod (pysces.PyscesModel.Event attribute) (pysces.PyscesModel.EventAssignment attribute) (pysces.PyscesModel.Function attribute) (pysces.PyscesModel.ReactionObj attribute) mod_data (pysces.PyscesModel.ScanDataObj attribute) mod_data_labels (pysces.PyscesModel.ScanDataObj attribute) model (pysces.PyscesScan.PITCONScanUtils attribute) ModelLoad() (pysces.PyscesModel.PysMod method) moduleDict (pysces.PyscesLink.SBWlink attribute) modules (pysces.PyscesLink.SBWlink attribute) MSG_PRINT_INTERVAL (pysces.PyscesScan.Scanner attribute)

N

name (pysces.PyscesModel.NewCoreBase attribute) (pysces.PyscesModel.PieceWise attribute) nan_on_bad_state (pysces.PyscesScan.Scanner attribute) NewCoreBase (class in pysces.PyscesModel)

NLEQ2() (pysces.PyscesModel.PysMod method) normal_timer() (pysces.PyscesUtils.TimerBox method) NumberBase (class in pysces.PyscesModel)

O

OPEN (pysces.PyscesModel.ScanDataObj attribute)

P

p_activateInterface() (pysces.PyscesPlot2.PyscesUPI method) p_deactivateInterface() (pysces.PyscesPlot2.PyscesUPI method) p_setInterface() (pysces.PyscesPlot2.PyscesUPI method) parameter_labels (pysces.PyscesModel.ScanDataObj attribute) parameters (pysces.PyscesModel.ScanDataObj attribute) ParGenSim() (pysces.PyscesModel.PysMod method) PAUSE_TIME (pysces.PyscesPlot2.GnuPlotUPI attribute) PieceWise (class in pysces.PyscesModel) piecewises (pysces.PyscesModel.Event attribute) (pysces.PyscesModel.EventAssignment attribute) (pysces.PyscesModel.Function attribute) (pysces.PyscesModel.ReactionObj attribute) PITCON() (pysces.PyscesModel.PysMod method) pitcon_range_high (pysces.PyscesScan.PITCONScanUtils attribute) pitcon_range_low (pysces.PyscesScan.PITCONScanUtils attribute) pitcon_res (pysces.PyscesScan.PITCONScanUtils attribute) pitcon_scan_density (pysces.PyscesScan.PITCONScanUtils attribute) pitcon_scan_parameter (pysces.PyscesScan.PITCONScanUtils attribute) pitcon_scan_parameter_3d (pysces.PyscesScan.PITCONScanUtils attribute) PITCONScanUtils (class in pysces.PyscesScan)

PivotSort() (pysces.PyscesStoich.Stoich method) PivotSort_initial() (pysces.PyscesStoich.Stoich method) plot() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) PlotBase (class in pysces.PyscesPlot2) plotLines() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) PLUfactorize() (pysces.PyscesStoich.Stoich method) psbw (pysces.PyscesLink.SBWlink attribute) pyplot (pysces.PyscesPlot2.MatplotlibUPI attribute) pysces.PyscesInterfaces (module) pysces.PyscesLink (module) pysces.PyscesModel (module) pysces.PyscesPlot2 (module) pysces.PyscesScan (module) pysces.PyscesStoich (module) pysces.PyscesUtils (module) PyscesUPI (class in pysces.PyscesPlot2) PysMod (class in pysces.PyscesModel)

Q

quietRun (pysces.PyscesScan.Scanner attribute)

R

rangeGen() (pysces.PyscesScan.Scanner method) rate (pysces.PyscesModel.ReactionObj attribute) rate_labels (pysces.PyscesModel.IntegrationDataObj attribute) rates (pysces.PyscesModel.IntegrationDataObj attribute) ReactionObj (class in pysces.PyscesModel) readMod2Core() (pysces.PyscesInterfaces.Core2interfaces method) readSBMLToCore() (pysces.PyscesInterfaces.Core2interfaces method) ReloadInitFunc() (pysces.PyscesModel.PysMod method) ReloadUserFunc() (pysces.PyscesModel.PysMod method) replot() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.PyscesUPI method) replotAndWait() (pysces.PyscesPlot2.GnuPlotUPI method) res_eigen (pysces.PyscesScan.PITCONScanUtils attribute) res_flux (pysces.PyscesScan.PITCONScanUtils attribute) res_idx (pysces.PyscesScan.PITCONScanUtils attribute)

res_metab (pysces.PyscesScan.PITCONScanUtils attribute) res_user (pysces.PyscesScan.PITCONScanUtils attribute) reset() (pysces.PyscesModel.Event method) reset_step() (pysces.PyscesUtils.TimerBox method) resetInputParameters() (pysces.PyscesScan.Scanner method) ResetNumberFormat() (pysces.PyscesModel.PysMod method) ridx (pysces.PyscesStoich.StructMatrix attribute) row (pysces.PyscesModel.BagOfStuff attribute) (pysces.PyscesStoich.StructMatrix attribute) rules (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute) rules_labels (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute) Run() (pysces.PyscesScan.Scanner method) RunAgain() (pysces.PyscesScan.Scanner method) runContinuation() (pysces.PyscesScan.PITCONScanUtils method)

S

save() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) sbml (pysces.PyscesInterfaces.Core2interfaces attribute) (pysces.PyscesLink.SBWLayoutWebLink attribute) sbml2core (pysces.PyscesInterfaces.Core2interfaces attribute) sbml_level (pysces.PyscesInterfaces.Core2interfaces attribute) sbml_version (pysces.PyscesInterfaces.Core2interfaces attribute) sbmllayout (pysces.PyscesLink.SBWLayoutWebLink attribute) sbw (pysces.PyscesLink.SBWlink attribute) SBW_exposeAll() (pysces.PyscesLink.SBWlink method) SBW_getActiveModules() (pysces.PyscesLink.SBWlink method) SBW_loadModule() (pysces.PyscesLink.SBWlink method) sbwhost (pysces.PyscesLink.SBWLayoutWebLink attribute) SBWLayoutWebLink (class in pysces.PyscesLink) SBWlink (class in pysces.PyscesLink) sbwModuleProxy (pysces.PyscesLink.SBWlink attribute) ScaleKL() (pysces.PyscesModel.PysMod method) ScalePivots() (pysces.PyscesStoich.Stoich method) scan (pysces.PyscesModel.PysMod attribute) Scan1() (pysces.PyscesModel.PysMod method) Scan1Plot() (pysces.PyscesModel.PysMod method) Scan2D() (pysces.PyscesModel.PysMod method) Scan2DPlot() (pysces.PyscesModel.PysMod method) ScanDataObj (class in pysces.PyscesModel) Scanner (class in pysces.PyscesScan) select() (pysces.PyscesModel.BagOfStuff method) SerialDecode() (pysces.PyscesModel.PysMod method) SerialEncode() (pysces.PyscesModel.PysMod method) set() (pysces.PyscesPlot2.GnuPlotUPI method) setArg() (pysces.PyscesModel.Function method) setAssignment() (pysces.PyscesModel.Event method) setAxisLabel() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) setByIdx() (pysces.PyscesStoich.StructMatrix method) setByName() (pysces.PyscesStoich.StructMatrix method) setCol() (pysces.PyscesStoich.StructMatrix method) setDataFileNumberFormat() (pysces.PyscesPlot2.GnuPlotUPI method) setFluxes() (pysces.PyscesModel.StateDataObj method) setFormula() (pysces.PyscesModel.EventAssignment method) setGraphTitle() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) setGrid() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) setKey() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) setKineticLaw() (pysces.PyscesModel.ReactionObj method) setLabels() (pysces.PyscesModel.IntegrationDataObj method) (pysces.PyscesModel.ScanDataObj method) setLineWidth() (pysces.PyscesPlot2.MatplotlibUPI method) setLogScale() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) SetLoud() (pysces.PyscesModel.PysMod method) setModValue() (pysces.PyscesScan.Scanner method) setMultiplot() (pysces.PyscesPlot2.GnuPlotUPI method) setName() (pysces.PyscesModel.NewCoreBase method) setNoLogScale() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) setOrigin() (pysces.PyscesPlot2.GnuPlotUPI method) setProxy() (pysces.PyscesLink.SBWLayoutWebLink method) SetQuiet() (pysces.PyscesModel.PysMod method) setRange() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.MatplotlibUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) setRates() (pysces.PyscesModel.IntegrationDataObj method) setRow() (pysces.PyscesStoich.StructMatrix method) setRules() (pysces.PyscesModel.IntegrationDataObj method) (pysces.PyscesModel.StateDataObj method) setSize() (pysces.PyscesPlot2.GnuPlotUPI method) setSizeAndOrigin() (pysces.PyscesPlot2.GnuPlotUPI method) setSpecies() (pysces.PyscesModel.IntegrationDataObj method) (pysces.PyscesModel.StateDataObj method) SetStateSymb() (pysces.PyscesModel.PysMod method) setTerminal() (pysces.PyscesPlot2.GnuPlotUPI method) setTime() (pysces.PyscesModel.IntegrationDataObj method) setTrigger() (pysces.PyscesModel.Event method)

setUserOuput() (pysces.PyscesScan.PITCONScanUtils method) setValue() (pysces.PyscesModel.NumberBase method) setVariable() (pysces.PyscesModel.EventAssignment method) setXData() (pysces.PyscesModel.IntegrationDataObj method) (pysces.PyscesModel.StateDataObj method) shape (pysces.PyscesStoich.StructMatrix attribute) showCC() (pysces.PyscesModel.PysMod method) showConserved() (pysces.PyscesModel.PysMod method) showEigen() (pysces.PyscesModel.PysMod method) showElas() (pysces.PyscesModel.PysMod method) showEModes() (pysces.PyscesLink.METATOOLlink method) showEpar() (pysces.PyscesModel.PysMod method) showEvar() (pysces.PyscesModel.PysMod method) showFluxRelationships() (pysces.PyscesModel.PysMod method) showK() (pysces.PyscesModel.PysMod method) showL() (pysces.PyscesModel.PysMod method) showModel() (pysces.PyscesModel.PysMod method) showModifiers() (pysces.PyscesModel.PysMod method) showN() (pysces.PyscesModel.PysMod method) showNr() (pysces.PyscesModel.PysMod method) showODE() (pysces.PyscesModel.PysMod method) showODEr() (pysces.PyscesModel.PysMod method) showPar() (pysces.PyscesModel.PysMod method) showRate() (pysces.PyscesModel.PysMod method) showRateEq() (pysces.PyscesModel.PysMod method) showSpecies() (pysces.PyscesModel.PysMod method) showSpeciesFixed() (pysces.PyscesModel.PysMod method) showSpeciesI() (pysces.PyscesModel.PysMod method) showState() (pysces.PyscesModel.PysMod method) SimPlot() (pysces.PyscesModel.PysMod method) Simulate() (pysces.PyscesModel.PysMod method) species (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute) species_labels (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute) SplitLU() (pysces.PyscesStoich.Stoich method) splot() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) splotSurfaces() (pysces.PyscesPlot2.GnuPlotUPI method) (pysces.PyscesPlot2.PlotBase method) (pysces.PyscesPlot2.PyscesUPI method) state (pysces.PyscesModel.Event attribute) State() (pysces.PyscesModel.PysMod method) state0 (pysces.PyscesModel.Event attribute) StateDataObj (class in pysces.PyscesModel) step_timer() (pysces.PyscesUtils.TimerBox method) stepGen() (pysces.PyscesScan.Scanner method) Stoich (class in pysces.PyscesStoich) Stoich_nmatrix_SetValue() (pysces.PyscesModel.PysMod method) Stoichiometry_Analyse() (pysces.PyscesModel.PysMod method) Stoichiometry_Init() (pysces.PyscesModel.PysMod method) Stoichiometry_Load_Serial() (pysces.PyscesModel.PysMod method) Stoichiometry_ReAnalyse() (pysces.PyscesModel.PysMod method) Stoichiometry_Save_Serial() (pysces.PyscesModel.PysMod method) stop() (pysces.PyscesUtils.TimerBox method) StoreData() (pysces.PyscesScan.Scanner method) str2bool() (in module pysces.PyscesUtils) StructMatrix (class in pysces.PyscesStoich) SVD_Rank_Check() (pysces.PyscesStoich.Stoich method) svg (pysces.PyscesLink.SBWLayoutWebLink attribute) SwapCol() (pysces.PyscesStoich.MathArrayFunc method) SwapCold() (pysces.PyscesStoich.MathArrayFunc method) SwapColz() (pysces.PyscesStoich.MathArrayFunc method) SwapElem() (pysces.PyscesStoich.MathArrayFunc method) SwapRow() (pysces.PyscesStoich.MathArrayFunc method) SwapRowd() (pysces.PyscesStoich.MathArrayFunc method) SwapRowz() (pysces.PyscesStoich.MathArrayFunc method) symbols (pysces.PyscesModel.Event attribute) (pysces.PyscesModel.EventAssignment attribute) (pysces.PyscesModel.Function attribute) (pysces.PyscesModel.ReactionObj attribute)

T

Terminals (pysces.PyscesPlot2.GnuPlotUPI attribute) testInputParameter() (pysces.PyscesScan.Scanner method) TestSimState() (pysces.PyscesModel.PysMod method) time (pysces.PyscesModel.IntegrationDataObj attribute) time_label (pysces.PyscesModel.IntegrationDataObj attribute)

timer (pysces.PyscesScan.PITCONScanUtils attribute) TimerBox (class in pysces.PyscesUtils) trigger (pysces.PyscesModel.Event attribute) TYPE_INFO (pysces.PyscesModel.IntegrationDataObj attribute)

U

unset() (pysces.PyscesPlot2.GnuPlotUPI method) unsetMultiplot() (pysces.PyscesPlot2.GnuPlotUPI method) urlGET() (pysces.PyscesLink.SBWLayoutWebLink method) urlPOST() (pysces.PyscesLink.SBWLayoutWebLink method)

USE_QR (pysces.PyscesStoich.Stoich attribute) User_Function() (pysces.PyscesModel.PysMod method) user_output (pysces.PyscesScan.PITCONScanUtils attribute)

V

value (pysces.PyscesModel.Function attribute) (pysces.PyscesModel.NumberBase attribute) (pysces.PyscesModel.PieceWise attribute) value_initial (pysces.PyscesModel.NumberBase attribute)

variable (pysces.PyscesModel.EventAssignment attribute) VersionCheck() (in module pysces.PyscesUtils)

W

wait() (pysces.PyscesPlot2.PlotBase method) WasteManagement (class in pysces.PyscesModel) Write_array() (pysces.PyscesModel.PysMod method) Write_array_html() (pysces.PyscesModel.PysMod method) Write_array_latex() (pysces.PyscesModel.PysMod method)

writeCore2PSC() (pysces.PyscesInterfaces.Core2interfaces method) writeCore2SBML() (pysces.PyscesInterfaces.Core2interfaces method) writeMod2PSC() (pysces.PyscesInterfaces.Core2interfaces method) writeMod2SBML() (pysces.PyscesInterfaces.Core2interfaces method) WriteOutput (class in pysces.PyscesUtils)

X

xcode (pysces.PyscesModel.Event attribute) (pysces.PyscesModel.EventAssignment attribute) (pysces.PyscesModel.Function attribute) (pysces.PyscesModel.PieceWise attribute) (pysces.PyscesModel.ReactionObj attribute) xdata (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute)

xdata_labels (pysces.PyscesModel.IntegrationDataObj attribute) (pysces.PyscesModel.ScanDataObj attribute) (pysces.PyscesModel.StateDataObj attribute)