Index

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)