Index

A

AnalysisRunner (class in rand_wc_model_gen.analysis.core) AnalyzeController (class in rand_wc_model_gen.__main__) AnalyzeController.Meta (class in rand_wc_model_gen.__main__) App (class in rand_wc_model_gen.__main__)

App.Meta (class in rand_wc_model_gen.__main__) arguments (rand_wc_model_gen.__main__.AnalyzeController.Meta attribute) (rand_wc_model_gen.__main__.BaseController.Meta attribute) (rand_wc_model_gen.__main__.GenerateController.Meta attribute) (rand_wc_model_gen.__main__.SimulateController.Meta attribute)

B

base_controller (rand_wc_model_gen.__main__.App.Meta attribute)

BaseController (class in rand_wc_model_gen.__main__) BaseController.Meta (class in rand_wc_model_gen.__main__)

C

ChromosomesGenesTusGenerator (class in rand_wc_model_gen.kb_gen.chrs_genes_tus) clean_and_validate_options() (rand_wc_model_gen.kb_gen.chrs_genes_tus.ChromosomesGenesTusGenerator method) (rand_wc_model_gen.kb_gen.compartments.CompartmentsGenerator method) (rand_wc_model_gen.kb_gen.core.KbGenerator method) (rand_wc_model_gen.kb_gen.genome.GenomeGenerator method) (rand_wc_model_gen.kb_gen.metabolites.MetabolitesGenerator method) (rand_wc_model_gen.kb_gen.observables.ObservablesGenerator method) (rand_wc_model_gen.kb_gen.properties.PropertiesGenerator method) (rand_wc_model_gen.kb_gen.rna.RnaGenerator method) (rand_wc_model_gen.model_gen.core.RandModelGen method)

CompartmentsGenerator (class in rand_wc_model_gen.kb_gen.compartments)

D

DEFAULT_ANALYSES (rand_wc_model_gen.analysis.core.AnalysisRunner attribute) DEFAULT_COMPONENT_GENERATORS (rand_wc_model_gen.kb_gen.core.KbGenerator attribute) description (rand_wc_model_gen.__main__.AnalyzeController.Meta attribute) (rand_wc_model_gen.__main__.BaseController.Meta attribute) (rand_wc_model_gen.__main__.GenerateController.Meta attribute) (rand_wc_model_gen.__main__.SimulateController.Meta attribute)

G

gen_cell_options() (rand_wc_model_gen.model_gen.core.RandModelGen method) gen_compartments() (rand_wc_model_gen.model_gen.core.RandModelGen method) gen_components() (rand_wc_model_gen.kb_gen.chrs_genes_tus.ChromosomesGenesTusGenerator method) (rand_wc_model_gen.kb_gen.compartments.CompartmentsGenerator method) (rand_wc_model_gen.kb_gen.genome.GenomeGenerator method) (rand_wc_model_gen.kb_gen.metabolites.MetabolitesGenerator method) (rand_wc_model_gen.kb_gen.observables.ObservablesGenerator method) (rand_wc_model_gen.kb_gen.properties.PropertiesGenerator method) (rand_wc_model_gen.kb_gen.rna.RnaGenerator method) gen_genome() (rand_wc_model_gen.kb_gen.genome.GenomeGenerator method) gen_reactions() (rand_wc_model_gen.model_gen.core.RandModelGen method) gen_rnas_proteins() (rand_wc_model_gen.kb_gen.genome.GenomeGenerator method)

gen_species() (rand_wc_model_gen.model_gen.core.RandModelGen method) gen_submodels() (rand_wc_model_gen.model_gen.core.RandModelGen method) gen_tus() (rand_wc_model_gen.kb_gen.genome.GenomeGenerator method) GenerateController (class in rand_wc_model_gen.__main__) GenerateController.Meta (class in rand_wc_model_gen.__main__) GenomeGenerator (class in rand_wc_model_gen.kb_gen.genome) get_config() (in module rand_wc_model_gen.config.core) get_data() (rand_wc_model_gen.kb_gen.metabolites.MetabolitesGenerator method) get_rate_law_compartment_context() (rand_wc_model_gen.model_gen.core.RandModelGen class method) get_rate_law_context() (rand_wc_model_gen.model_gen.core.RandModelGen class method) get_rate_law_function_context() (rand_wc_model_gen.model_gen.core.RandModelGen class method) get_rate_law_parameter_context() (rand_wc_model_gen.model_gen.core.RandModelGen class method) get_rate_law_species_context() (rand_wc_model_gen.model_gen.core.RandModelGen class method)

H

handlers (rand_wc_model_gen.__main__.App.Meta attribute) help (rand_wc_model_gen.__main__.AnalyzeController.Meta attribute) (rand_wc_model_gen.__main__.BaseController.Meta attribute) (rand_wc_model_gen.__main__.GenerateController.Meta attribute) (rand_wc_model_gen.__main__.SimulateController.Meta attribute)

K

KbGenerator (class in rand_wc_model_gen.kb_gen.core)

L

label (rand_wc_model_gen.__main__.AnalyzeController.Meta attribute) (rand_wc_model_gen.__main__.App.Meta attribute) (rand_wc_model_gen.__main__.BaseController.Meta attribute) (rand_wc_model_gen.__main__.GenerateController.Meta attribute) (rand_wc_model_gen.__main__.SimulateController.Meta attribute)

M

main() (in module rand_wc_model_gen.__main__)

MetabolitesGenerator (class in rand_wc_model_gen.kb_gen.metabolites)

O

ObservablesGenerator (class in rand_wc_model_gen.kb_gen.observables)

options (rand_wc_model_gen.model_gen.core.RandModelGen attribute)

P

plot() (in module rand_wc_model_gen.model_gen.core) plot_individual_rna() (rand_wc_model_gen.analysis.sim.rna.RnaSimulationAnalysis method)

plot_total_rna() (rand_wc_model_gen.analysis.sim.rna.RnaSimulationAnalysis method) PropertiesGenerator (class in rand_wc_model_gen.kb_gen.properties)

R

rand() (rand_wc_model_gen.kb_gen.chrs_genes_tus.ChromosomesGenesTusGenerator method) (rand_wc_model_gen.kb_gen.genome.GenomeGenerator method) (rand_wc_model_gen.model_gen.core.RandModelGen method) rand_wc_model_gen (module) rand_wc_model_gen.__main__ (module) rand_wc_model_gen._version (module) rand_wc_model_gen.analysis (module) rand_wc_model_gen.analysis.core (module) rand_wc_model_gen.analysis.kb (module) rand_wc_model_gen.analysis.model (module) rand_wc_model_gen.analysis.sim (module) rand_wc_model_gen.analysis.sim.rna (module) rand_wc_model_gen.config (module) rand_wc_model_gen.config.core (module) rand_wc_model_gen.kb_gen (module) rand_wc_model_gen.kb_gen.chrs_genes_tus (module)

rand_wc_model_gen.kb_gen.compartments (module) rand_wc_model_gen.kb_gen.core (module) rand_wc_model_gen.kb_gen.genome (module) rand_wc_model_gen.kb_gen.metabolites (module) rand_wc_model_gen.kb_gen.observables (module) rand_wc_model_gen.kb_gen.properties (module) rand_wc_model_gen.kb_gen.rna (module) rand_wc_model_gen.model_gen (module) rand_wc_model_gen.model_gen.core (module) RandModelGen (class in rand_wc_model_gen.model_gen.core) results (rand_wc_model_gen.__main__.App attribute) RnaGenerator (class in rand_wc_model_gen.kb_gen.rna) RnaSimulationAnalysis (class in rand_wc_model_gen.analysis.sim.rna) run() (rand_wc_model_gen.analysis.sim.rna.RnaSimulationAnalysis method) (rand_wc_model_gen.kb_gen.core.KbGenerator method) (rand_wc_model_gen.model_gen.core.RandModelGen method) run_with_options() (rand_wc_model_gen.model_gen.core.RandModelGen method)

S

SimulateController (class in rand_wc_model_gen.__main__) SimulateController.Meta (class in rand_wc_model_gen.__main__) stacked_on (rand_wc_model_gen.__main__.AnalyzeController.Meta attribute) (rand_wc_model_gen.__main__.GenerateController.Meta attribute) (rand_wc_model_gen.__main__.SimulateController.Meta attribute)

stacked_type (rand_wc_model_gen.__main__.AnalyzeController.Meta attribute) (rand_wc_model_gen.__main__.GenerateController.Meta attribute) (rand_wc_model_gen.__main__.SimulateController.Meta attribute)