PySCeS
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Introduction
Getting started
Modelling
Parameter scanning
Plotting
Displaying data
Installing and configuring
References
The PySCeS Model Description Language
PySCeS Module documentation
PySCeS
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Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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() (in module pysces.PyscesParScan)
(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_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
enableDataPandas() (pysces.PyscesModel.PysMod method)
enablePandas() (in module pysces)
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)
ExecRateRules() (pysces.PyscesModel.PysMod method)
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)
flush() (in module pysces.PyscesParScan)
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)
GatherScanResult() (pysces.PyscesParScan.ParScanner method)
genOn (pysces.PyscesParScan.ParScanner attribute)
(pysces.PyscesScan.Scanner attribute)
genScanSpace() (pysces.PyscesParScan.ParScanner method)
get() (pysces.PyscesModel.BagOfStuff 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)
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)
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.PyscesParScan.ParScanner attribute)
(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.PyscesParScan.ParScanner attribute)
(pysces.PyscesScan.Scanner attribute)
invalid_state_list_idx (pysces.PyscesParScan.ParScanner attribute)
(pysces.PyscesScan.Scanner attribute)
invalid_states (pysces.PyscesModel.ScanDataObj attribute)
IS_VALID (pysces.PyscesModel.IntegrationDataObj attribute)
(pysces.PyscesModel.StateDataObj attribute)
isnotebook() (pysces.PyscesPlot2.MatplotlibUPI method)
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)
mach_eps (pysces.PyscesStoich.Stoich 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)
module
pysces
pysces.PyscesInterfaces
pysces.PyscesLink
pysces.PyscesModel
pysces.PyscesParScan
pysces.PyscesPlot2
pysces.PyscesScan
pysces.PyscesStoich
pysces.PyscesUtils
moduleDict (pysces.PyscesLink.SBWlink attribute)
modules (pysces.PyscesLink.SBWlink attribute)
MSG_PRINT_INTERVAL (pysces.PyscesParScan.ParScanner attribute)
(pysces.PyscesScan.Scanner attribute)
N
name (pysces.PyscesModel.PieceWise attribute)
nan_on_bad_state (pysces.PyscesParScan.ParScanner attribute)
(pysces.PyscesScan.Scanner attribute)
NLEQ2() (pysces.PyscesModel.PysMod method)
normal_timer() (pysces.PyscesUtils.TimerBox method)
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)
ParScanner (class in pysces.PyscesParScan)
PAUSE_TIME (pysces.PyscesPlot2.GnuPlotUPI attribute)
persistent (pysces.PyscesModel.Event 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)
Prepare() (pysces.PyscesParScan.ParScanner method)
priority (pysces.PyscesModel.Event attribute)
psbw (pysces.PyscesLink.SBWlink attribute)
pyplot (pysces.PyscesPlot2.MatplotlibUPI attribute)
pysces
module
pysces.PyscesInterfaces
module
pysces.PyscesLink
module
pysces.PyscesModel
module
pysces.PyscesParScan
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
random (pysces.PyscesModel.PysMod attribute)
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)
reLoad() (pysces.PyscesModel.PysMod 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.PyscesParScan.ParScanner method)
(pysces.PyscesScan.Scanner method)
RunAgain() (pysces.PyscesScan.Scanner method)
runContinuation() (pysces.PyscesScan.PITCONScanUtils method)
RunScatter() (pysces.PyscesParScan.ParScanner 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 property)
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)
scans_per_run (pysces.PyscesParScan.ParScanner attribute)
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() (in module pysces.PyscesParScan)
(pysces.PyscesScan.Scanner method)
setMultiplot() (pysces.PyscesPlot2.GnuPlotUPI method)
setNoLogScale() (pysces.PyscesPlot2.GnuPlotUPI method)
(pysces.PyscesPlot2.MatplotlibUPI method)
(pysces.PyscesPlot2.PlotBase method)
(pysces.PyscesPlot2.PyscesUPI method)
setOrigin() (pysces.PyscesPlot2.GnuPlotUPI method)
setPersistent() (pysces.PyscesModel.Event method)
setPriority() (pysces.PyscesModel.Event 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)
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)
sim (pysces.PyscesModel.PysMod property)
SimPlot() (pysces.PyscesModel.PysMod method)
Simulate() (pysces.PyscesModel.PysMod method)
smallest_normal (pysces.PyscesStoich.Stoich.finfo property)
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.finfo (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.PyscesParScan.ParScanner method)
(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)
tiny (pysces.PyscesStoich.Stoich.finfo property)
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.PieceWise 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)
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