Index

A

analyze_model() (wc_model_gen.core.ModelGenerator static method)

C

calc_aa_per_prot() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_aa_transfer_rate() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_avg_deg_rate() (in module wc_model_gen.utils) calc_avg_half_life() (wc_model_gen.prokaryote.initalize_model.InitalizeModel static method) calc_avg_syn_rate() (in module wc_model_gen.utils) calc_gtp_corr_rate() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_gtp_per_translate() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_h_per_transcript() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_h_transfer_rate() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_mpp_conversion_rate() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_mpp_transfer_rate() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_prot_copy_num() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_prot_degrad_rxns() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_rna_copy_num() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_rna_degrad_rxns() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calc_tpp_per_rna() (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) calibrate_submodel() (wc_model_gen.core.SubmodelGenerator method) (wc_model_gen.eukaryote.complexation.ComplexationSubmodelGenerator method) (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method) (wc_model_gen.eukaryote.protein_degradation.ProteinDegradationSubmodelGenerator method) (wc_model_gen.eukaryote.rna_degradation.RnaDegradationSubmodelGenerator method) (wc_model_gen.eukaryote.transcription.TranscriptionSubmodelGenerator method) (wc_model_gen.eukaryote.translation_translocation.TranslationTranslocationSubmodelGenerator method) (wc_model_gen.prokaryote.protein_degradation.ProteinDegradationSubmodelGenerator method) (wc_model_gen.prokaryote.rna_degradation.RnaDegradationSubmodelGenerator method) (wc_model_gen.prokaryote.transcription.TranscriptionSubmodelGenerator method) (wc_model_gen.prokaryote.translation.TranslationSubmodelGenerator method)

clean_and_validate_options() (wc_model_gen.core.ModelComponentGenerator method) (wc_model_gen.core.ModelGenerator method) (wc_model_gen.core.SubmodelGenerator method) (wc_model_gen.eukaryote.complexation.ComplexationSubmodelGenerator method) (wc_model_gen.eukaryote.core.EukaryoteModelGenerator method) (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method) (wc_model_gen.eukaryote.protein_degradation.ProteinDegradationSubmodelGenerator method) (wc_model_gen.eukaryote.rna_degradation.RnaDegradationSubmodelGenerator method) (wc_model_gen.eukaryote.transcription.TranscriptionSubmodelGenerator method) (wc_model_gen.eukaryote.translation_translocation.TranslationTranslocationSubmodelGenerator method) (wc_model_gen.prokaryote.core.ProkaryoteModelGenerator method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) (wc_model_gen.prokaryote.protein_degradation.ProteinDegradationSubmodelGenerator method) (wc_model_gen.prokaryote.rna_degradation.RnaDegradationSubmodelGenerator method) (wc_model_gen.prokaryote.transcription.TranscriptionSubmodelGenerator method) (wc_model_gen.prokaryote.translation.TranslationSubmodelGenerator method) ComplexationSubmodelGenerator (class in wc_model_gen.eukaryote.complexation) component_generators (wc_model_gen.core.ModelGenerator attribute) conv_for_optim() (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method)

D

DEFAULT_COMPONENT_GENERATORS (wc_model_gen.core.ModelGenerator attribute) (wc_model_gen.eukaryote.core.EukaryoteModelGenerator attribute) (wc_model_gen.prokaryote.core.ProkaryoteModelGenerator attribute)

determine_bounds() (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method) determine_initial_concentration() (wc_model_gen.eukaryote.complexation.ComplexationSubmodelGenerator method) determine_protein_structure_from_aa() (wc_model_gen.eukaryote.initialize_model.InitializeModel method)

E

EukaryoteModelGenerator (class in wc_model_gen.eukaryote.core)

F

flux_variability_analysis() (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method)

G

gen_compartments() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_complexes() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_distribution_init_concentrations() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_dna() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) gen_environment() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) gen_kb_rate_laws() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_kb_reactions() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_mass_action_rate_law() (in module wc_model_gen.utils) gen_metabolites() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_michaelis_menten_like_propensity_function() (in module wc_model_gen.utils) gen_michaelis_menten_like_rate_law() (in module wc_model_gen.utils) gen_observables() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_parameters() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_protein() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_rand_min_model_kb() (wc_model_gen.core.ModelGenerator static method) gen_rate_laws() (wc_model_gen.core.SubmodelGenerator method) (wc_model_gen.eukaryote.complexation.ComplexationSubmodelGenerator method) (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method) (wc_model_gen.eukaryote.protein_degradation.ProteinDegradationSubmodelGenerator method) (wc_model_gen.eukaryote.rna_degradation.RnaDegradationSubmodelGenerator method) (wc_model_gen.eukaryote.transcription.TranscriptionSubmodelGenerator method) (wc_model_gen.eukaryote.translation_translocation.TranslationTranslocationSubmodelGenerator method) (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) (wc_model_gen.prokaryote.protein_degradation.ProteinDegradationSubmodelGenerator method) (wc_model_gen.prokaryote.rna_degradation.RnaDegradationSubmodelGenerator method) (wc_model_gen.prokaryote.transcription.TranscriptionSubmodelGenerator method) (wc_model_gen.prokaryote.translation.TranslationSubmodelGenerator method)

gen_reactions() (wc_model_gen.core.SubmodelGenerator method) (wc_model_gen.eukaryote.complexation.ComplexationSubmodelGenerator method) (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method) (wc_model_gen.eukaryote.protein_degradation.ProteinDegradationSubmodelGenerator method) (wc_model_gen.eukaryote.rna_degradation.RnaDegradationSubmodelGenerator method) (wc_model_gen.eukaryote.transcription.TranscriptionSubmodelGenerator method) (wc_model_gen.eukaryote.translation_translocation.TranslationTranslocationSubmodelGenerator method) (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator method) (wc_model_gen.prokaryote.protein_degradation.ProteinDegradationSubmodelGenerator method) (wc_model_gen.prokaryote.rna_degradation.RnaDegradationSubmodelGenerator method) (wc_model_gen.prokaryote.transcription.TranscriptionSubmodelGenerator method) (wc_model_gen.prokaryote.translation.TranslationSubmodelGenerator method) gen_response_functions() (in module wc_model_gen.utils) gen_rna() (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_species_type() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method) gen_taxon() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) gen_transcripts() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) global_vars_from_input() (wc_model_gen.eukaryote.initialize_model.InitializeModel method)

I

impute_kinetic_constant() (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method)

InitalizeModel (class in wc_model_gen.prokaryote.initalize_model) InitializeModel (class in wc_model_gen.eukaryote.initialize_model)

K

knowledge_base (wc_model_gen.core.ModelComponentGenerator attribute) (wc_model_gen.core.ModelGenerator attribute) (wc_model_gen.core.SubmodelGenerator attribute)

M

MetabolismSubmodelGenerator (class in wc_model_gen.eukaryote.metabolism) (class in wc_model_gen.prokaryote.metabolism) model (wc_model_gen.core.ModelComponentGenerator attribute) (wc_model_gen.core.SubmodelGenerator attribute)

ModelComponentGenerator (class in wc_model_gen.core) ModelGenerator (class in wc_model_gen.core)

O

options (wc_model_gen.core.ModelComponentGenerator attribute) (wc_model_gen.core.ModelGenerator attribute) (wc_model_gen.core.SubmodelGenerator attribute)

P

populate_protein_aa_usage() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) ProkaryoteModelGenerator (class in wc_model_gen.prokaryote.core)

ProteinDegradationSubmodelGenerator (class in wc_model_gen.eukaryote.protein_degradation) (class in wc_model_gen.prokaryote.protein_degradation)

R

reaction_scale (wc_model_gen.prokaryote.metabolism.MetabolismSubmodelGenerator attribute) relax_bounds() (wc_model_gen.eukaryote.metabolism.MetabolismSubmodelGenerator method) RnaDegradationSubmodelGenerator (class in wc_model_gen.eukaryote.rna_degradation) (class in wc_model_gen.prokaryote.rna_degradation) run() (wc_model_gen.core.ModelComponentGenerator method) (wc_model_gen.core.ModelGenerator method) (wc_model_gen.core.SubmodelGenerator method) (wc_model_gen.eukaryote.initialize_model.InitializeModel method) (wc_model_gen.prokaryote.initalize_model.InitalizeModel method)

run_model() (wc_model_gen.core.ModelGenerator static method)

S

simple_activator() (in module wc_model_gen.utils) simple_repressor() (in module wc_model_gen.utils)

structure_to_smiles_and_props() (wc_model_gen.eukaryote.initialize_model.InitializeModel method) submodel (wc_model_gen.core.SubmodelGenerator attribute) SubmodelGenerator (class in wc_model_gen.core)

T

test_metabolite_production() (in module wc_model_gen.utils) TranscriptionSubmodelGenerator (class in wc_model_gen.eukaryote.transcription) (class in wc_model_gen.prokaryote.transcription)

TranslationSubmodelGenerator (class in wc_model_gen.prokaryote.translation) TranslationTranslocationSubmodelGenerator (class in wc_model_gen.eukaryote.translation_translocation)

W

wc_model_gen (module) wc_model_gen._version (module) wc_model_gen.core (module) wc_model_gen.eukaryote (module) wc_model_gen.eukaryote.complexation (module) wc_model_gen.eukaryote.core (module) wc_model_gen.eukaryote.initialize_model (module) wc_model_gen.eukaryote.metabolism (module) wc_model_gen.eukaryote.protein_degradation (module) wc_model_gen.eukaryote.rna_degradation (module) wc_model_gen.eukaryote.transcription (module)

wc_model_gen.eukaryote.translation_translocation (module) wc_model_gen.global_vars (module) wc_model_gen.prokaryote (module) wc_model_gen.prokaryote.core (module) wc_model_gen.prokaryote.initalize_model (module) wc_model_gen.prokaryote.metabolism (module) wc_model_gen.prokaryote.protein_degradation (module) wc_model_gen.prokaryote.rna_degradation (module) wc_model_gen.prokaryote.transcription (module) wc_model_gen.prokaryote.translation (module) wc_model_gen.utils (module)