pyRBM
0.3.0
pyRBM package
pyRBM
Index
Index
A
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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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L
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M
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O
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P
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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
A
addClass() (Classes method)
addEntry() (Trajectory method)
addLinearStoichiomety() (Rule method)
addRule() (Rules method)
addRules() (Rules method)
addSimplePropensityFunction() (Rule method)
addWaitTimeDistribution() (Rule method)
animate() (FrequencyBarChart method)
C
changeDate() (ModelState method)
changeModelClassValue() (ModelState method)
changeMonth() (ModelState method)
checkConditionDict() (ICompartment method)
checkParams() (Distribution method)
checkParamsLaplace() (Distribution method)
(DoublePowerLawDistribution method)
(ExponentialDistribution method)
(GammaDistribution method)
(GammaPowerLawDistribution method)
(ShiftedGammaPowerLawDistribution method)
(UniformPowerLawDistribution method)
checkRuleDefinition() (Rule method)
Classes (class in pyRBM.Build.Classes)
classes_path (ModelPaths attribute)
(ModelPaths property)
Compartment (class in pyRBM.Simulation.Compartment)
compartment_path (ModelPaths attribute)
compartments_path (ModelPaths property)
conf
module
createArgsDict() (in module pyRBM.Build.Utils)
createDistribution() (DistributionFactory method)
createEuclideanDistanceMatrix() (in module pyRBM.Build.Utils)
D
Distribution (class in pyRBM.Simulation.WaitTimeDistributions)
DistributionFactory (class in pyRBM.Simulation.WaitTimeDistributions)
DoublePowerLawDistribution (class in pyRBM.Simulation.WaitTimeDistributions)
E
ExitEntranceRule (class in pyRBM.Build.RuleTemplates)
ExponentialDistribution (class in pyRBM.Simulation.WaitTimeDistributions)
F
FrequencyBarChart (class in pyRBM.Core.Plotting)
G
GammaDistribution (class in pyRBM.Simulation.WaitTimeDistributions)
GammaPowerLawDistribution (class in pyRBM.Simulation.WaitTimeDistributions)
H
haversine() (in module pyRBM.Build.Utils)
I
ICompartment (class in pyRBM.Core.Interfaces)
isLaplaceGillespieCompatible() (Distribution method)
isNMGACompatible() (Distribution method)
isNonDefaultTargetArray() (in module pyRBM.Build.Rules)
isSubtypeOf() (in module pyRBM.Build.RuleMatching)
L
loadClasses() (in module pyRBM.Core.Cache)
loadCompartments() (in module pyRBM.Core.Cache)
loadCompartmentsFromJSONFile() (LoadedCompartments method)
LoadedCompartments (class in pyRBM.Build.ProcessDescriptionFiles)
loadMatchedRules() (in module pyRBM.Core.Cache)
M
matched_rules_path (ModelPaths attribute)
(ModelPaths property)
metarule_path (ModelPaths attribute)
metarules_path (ModelPaths property)
MittagLefflerDistribution (class in pyRBM.Simulation.WaitTimeDistributions)
ModelPaths (class in pyRBM.Core.Cache)
ModelState (class in pyRBM.Simulation.State)
module
conf
pyRBM
pyRBM.Analysis
pyRBM.Build
pyRBM.Build.Classes
pyRBM.Build.ProcessDescriptionFiles
pyRBM.Build.RuleMatching
pyRBM.Build.Rules
pyRBM.Build.RuleTemplates
pyRBM.Build.Utils
pyRBM.Core
pyRBM.Core.Cache
pyRBM.Core.Interfaces
pyRBM.Core.Plotting
pyRBM.Core.StringUtilities
pyRBM.Examples
pyRBM.Simulation
pyRBM.Simulation.Compartment
pyRBM.Simulation.Rule
pyRBM.Simulation.RuleChain
pyRBM.Simulation.State
pyRBM.Simulation.Trajectory
pyRBM.Simulation.WaitTimeDistributions
source
source.conf
O
obtainPropensity() (in module pyRBM.Build.RuleMatching)
obtainStochiometry() (in module pyRBM.Build.RuleMatching)
P
parseVarName() (in module pyRBM.Core.StringUtilities)
partial_evaluation() (Rule method)
plotAllClassesOverTime() (Trajectory method)
processDistributionString() (in module pyRBM.Simulation.WaitTimeDistributions)
processFilenameOrDict() (in module pyRBM.Core.Cache)
processUpdate() (ModelState method)
pyRBM
module
pyRBM.Analysis
module
pyRBM.Build
module
pyRBM.Build.Classes
module
pyRBM.Build.ProcessDescriptionFiles
module
pyRBM.Build.RuleMatching
module
pyRBM.Build.Rules
module
pyRBM.Build.RuleTemplates
module
pyRBM.Build.Utils
module
pyRBM.Core
module
pyRBM.Core.Cache
module
pyRBM.Core.Interfaces
module
pyRBM.Core.Plotting
module
pyRBM.Core.StringUtilities
module
pyRBM.Examples
module
pyRBM.Simulation
module
pyRBM.Simulation.Compartment
module
pyRBM.Simulation.Rule
module
pyRBM.Simulation.RuleChain
module
pyRBM.Simulation.State
module
pyRBM.Simulation.Trajectory
module
pyRBM.Simulation.WaitTimeDistributions
module
R
readDictFromJSON() (in module pyRBM.Core.Cache)
removeTypeRequirement() (Rules method)
replaceVarName() (in module pyRBM.Core.StringUtilities)
reset() (Compartment method)
(ModelState method)
resetClassVars() (ModelState method)
returnBuiltInClasses() (Classes method)
returnChangedVars() (ModelState method)
returnClassDict() (Classes method)
returnEventRate() (Rule method)
returnLaplaceRate() (Distribution method)
returnMatchedRulesDict() (in module pyRBM.Build.RuleMatching)
returnMetaRuleDict() (Rules method)
returnModelClasses() (ModelState method)
returnModelClassesValues() (ModelState method)
returnOneStepRuleUpdates() (in module pyRBM.Simulation.RuleChain)
returnPropensity() (Rule method)
returnRandomLaplaceFunc() (Distribution method)
(DoublePowerLawDistribution method)
(ExponentialDistribution method)
(GammaDistribution method)
(GammaPowerLawDistribution method)
(ShiftedGammaPowerLawDistribution method)
(UniformPowerLawDistribution method)
returnRandomNMGAFunc() (Distribution method)
returnRate() (Distribution method)
returnRuleDict() (Rule method)
returnRuleMatchingIndices() (in module pyRBM.Build.RuleMatching)
returnStringRepr() (Distribution method)
returnSympyClassVarsDict() (in module pyRBM.Build.Rules)
Rule (class in pyRBM.Build.Rules)
(class in pyRBM.Simulation.Rule)
Rules (class in pyRBM.Build.Rules)
S
save_model_folder (ModelPaths attribute)
setConstants() (ICompartment method)
setInitialConditions() (ICompartment method)
ShiftedGammaPowerLawDistribution (class in pyRBM.Simulation.WaitTimeDistributions)
SingleLocationProductionRule (class in pyRBM.Build.RuleTemplates)
SingleLocationRule (class in pyRBM.Build.RuleTemplates)
SolverDataPlotting (class in pyRBM.Core.Plotting)
source
module
source.conf
module
T
tba() (MittagLefflerDistribution method)
Trajectory (class in pyRBM.Simulation.Trajectory)
TransportRule (class in pyRBM.Build.RuleTemplates)
triggerAttemptedRuleChange() (Rule method)
U
UniformPowerLawDistribution (class in pyRBM.Simulation.WaitTimeDistributions)
updateCompartmentValues() (Compartment method)
V
validateFormula() (Rule method)
W
writeDictToJSON() (in module pyRBM.Core.Cache)