Index

A

App (class in h1_hesc.__main__)

App.Meta (class in h1_hesc.__main__) arguments (h1_hesc.__main__.BaseController.Meta attribute)

B

base_controller (h1_hesc.__main__.App.Meta attribute)

BaseController (class in h1_hesc.__main__) BaseController.Meta (class in h1_hesc.__main__)

C

calc_eff_vmax() (in module h1_hesc.utils) calc_median_kcat() (in module h1_hesc.utils) ChromosomesGenerator (class in h1_hesc.kb_gen.chromosomes) clean_and_validate_options() (h1_hesc.kb_gen.chromosomes.ChromosomesGenerator method) (h1_hesc.kb_gen.compartments.CompartmentsGenerator method) (h1_hesc.kb_gen.complexes.ComplexesGenerator method) (h1_hesc.kb_gen.core.KbGenerator method) (h1_hesc.kb_gen.genes_transcripts_exons_proteins.GenesTranscriptsExonsProteinsGenerator method) (h1_hesc.kb_gen.metabolic_network.MetabolicNetworkGenerator method) (h1_hesc.kb_gen.metabolic_reaction_kinetics.MetabolicReactionKineticsGenerator method) (h1_hesc.kb_gen.metabolites.MetabolitesGenerator method) (h1_hesc.kb_gen.properties.PropertiesGenerator method) (h1_hesc.kb_gen.protein_modifications.ProteinModificationsGenerator method) (h1_hesc.kb_gen.proteins.ProteinsGenerator method) (h1_hesc.kb_gen.regulatory_modules.RegulatoryModulesGenerator method) (h1_hesc.kb_gen.taxon.TaxonGenerator method) (h1_hesc.kb_gen.transcripts.TranscriptsGenerator method) (h1_hesc.model_gen.complexation_option.ComplexationOptionGenerator method) (h1_hesc.model_gen.core.H1ModelGenerator method) (h1_hesc.model_gen.core.SubmodelOptionComponentGenerator method) (h1_hesc.model_gen.initialize_model_option.InitializeModelOptionGenerator method) (h1_hesc.model_gen.metabolism_option.MetabolismOptionGenerator method) (h1_hesc.model_gen.protein_degradation_option.ProteinDegradationOptionGenerator method) (h1_hesc.model_gen.rna_degradation_option.RnaDegradationOptionGenerator method) (h1_hesc.model_gen.transcription_option.TranscriptionOptionGenerator method) (h1_hesc.model_gen.translation_translocation_option.TranslationTranslocationOptionGenerator method) (h1_hesc.scaled_down_model.kb_core.KbGenerator method)

compare_essentiality() (in module h1_hesc.model_sim.essentiality) CompartmentsGenerator (class in h1_hesc.kb_gen.compartments) ComplexationOptionGenerator (class in h1_hesc.model_gen.complexation_option) ComplexesGenerator (class in h1_hesc.kb_gen.complexes) component_options (h1_hesc.model_gen.core.OptionComponentGenerator attribute) (h1_hesc.model_gen.core.SubmodelOptionComponentGenerator attribute) create_conv_model() (in module h1_hesc.utils)

D

decay() (h1_hesc.__main__.BaseController method) DEFAULT_COMPONENT_GENERATORS (h1_hesc.kb_gen.core.KbGenerator attribute) (h1_hesc.scaled_down_model.kb_core.KbGenerator attribute)

DEFAULT_OPTION_GENERATORS (h1_hesc.model_gen.core.OptionGenerator attribute) description (h1_hesc.__main__.BaseController.Meta attribute) determine_bounds() (in module h1_hesc.utils)

E

essential() (h1_hesc.__main__.BaseController method) essentiality_simulation() (in module h1_hesc.model_sim.essentiality)

eval_gene_reaction_rule() (in module h1_hesc.utils) extract_info_from_string() (in module h1_hesc.utils)

G

gen_components() (h1_hesc.kb_gen.chromosomes.ChromosomesGenerator method) (h1_hesc.kb_gen.compartments.CompartmentsGenerator method) (h1_hesc.kb_gen.complexes.ComplexesGenerator method) (h1_hesc.kb_gen.genes_transcripts_exons_proteins.GenesTranscriptsExonsProteinsGenerator method) (h1_hesc.kb_gen.metabolic_network.MetabolicNetworkGenerator method) (h1_hesc.kb_gen.metabolic_reaction_kinetics.MetabolicReactionKineticsGenerator method) (h1_hesc.kb_gen.metabolites.MetabolitesGenerator method) (h1_hesc.kb_gen.properties.PropertiesGenerator method) (h1_hesc.kb_gen.protein_modifications.ProteinModificationsGenerator method) (h1_hesc.kb_gen.proteins.ProteinsGenerator method) (h1_hesc.kb_gen.regulatory_modules.RegulatoryModulesGenerator method) (h1_hesc.kb_gen.taxon.TaxonGenerator method) (h1_hesc.kb_gen.transcripts.TranscriptsGenerator method) gen_options() (h1_hesc.model_gen.complexation_option.ComplexationOptionGenerator method) (h1_hesc.model_gen.core.SubmodelOptionComponentGenerator method) (h1_hesc.model_gen.initialize_model_option.InitializeModelOptionGenerator method) (h1_hesc.model_gen.metabolism_option.MetabolismOptionGenerator method) (h1_hesc.model_gen.protein_degradation_option.ProteinDegradationOptionGenerator method) (h1_hesc.model_gen.rna_degradation_option.RnaDegradationOptionGenerator method) (h1_hesc.model_gen.transcription_option.TranscriptionOptionGenerator method) (h1_hesc.model_gen.translation_translocation_option.TranslationTranslocationOptionGenerator method) GenesTranscriptsExonsProteinsGenerator (class in h1_hesc.kb_gen.genes_transcripts_exons_proteins) get_complexes_from_gene_rule() (in module h1_hesc.utils) get_data() (h1_hesc.kb_gen.chromosomes.ChromosomesGenerator method) (h1_hesc.kb_gen.compartments.CompartmentsGenerator method) (h1_hesc.kb_gen.complexes.ComplexesGenerator method) (h1_hesc.kb_gen.genes_transcripts_exons_proteins.GenesTranscriptsExonsProteinsGenerator method) (h1_hesc.kb_gen.metabolic_network.MetabolicNetworkGenerator method) (h1_hesc.kb_gen.metabolic_reaction_kinetics.MetabolicReactionKineticsGenerator method) (h1_hesc.kb_gen.metabolites.MetabolitesGenerator method) (h1_hesc.kb_gen.properties.PropertiesGenerator method) (h1_hesc.kb_gen.protein_modifications.ProteinModificationsGenerator method) (h1_hesc.kb_gen.proteins.ProteinsGenerator method) (h1_hesc.kb_gen.regulatory_modules.RegulatoryModulesGenerator method) (h1_hesc.kb_gen.taxon.TaxonGenerator method) (h1_hesc.kb_gen.transcripts.TranscriptsGenerator method) (h1_hesc.model_gen.complexation_option.ComplexationOptionGenerator method) (h1_hesc.model_gen.core.SubmodelOptionComponentGenerator method) (h1_hesc.model_gen.initialize_model_option.InitializeModelOptionGenerator method) (h1_hesc.model_gen.metabolism_option.MetabolismOptionGenerator method) (h1_hesc.model_gen.protein_degradation_option.ProteinDegradationOptionGenerator method) (h1_hesc.model_gen.rna_degradation_option.RnaDegradationOptionGenerator method) (h1_hesc.model_gen.transcription_option.TranscriptionOptionGenerator method) (h1_hesc.model_gen.translation_translocation_option.TranslationTranslocationOptionGenerator method)

get_enzyme_equation() (in module h1_hesc.utils) get_reaction_equation() (in module h1_hesc.utils) get_value_inchi_formula_connectivity() (in module h1_hesc.utils) growth_decay() (h1_hesc.__main__.BaseController method)

H

h1_hesc (module) h1_hesc.__main__ (module) h1_hesc._version (module) h1_hesc.data (module) h1_hesc.data.recon_2_2 (module) h1_hesc.kb_gen (module) h1_hesc.kb_gen.chromosomes (module) h1_hesc.kb_gen.compartments (module) h1_hesc.kb_gen.complexes (module) h1_hesc.kb_gen.core (module) h1_hesc.kb_gen.genes_transcripts_exons_proteins (module) h1_hesc.kb_gen.metabolic_network (module) h1_hesc.kb_gen.metabolic_reaction_kinetics (module) h1_hesc.kb_gen.metabolites (module) h1_hesc.kb_gen.properties (module) h1_hesc.kb_gen.protein_modifications (module) h1_hesc.kb_gen.proteins (module) h1_hesc.kb_gen.regulatory_modules (module) h1_hesc.kb_gen.taxon (module) h1_hesc.kb_gen.transcripts (module)

h1_hesc.model_gen (module) h1_hesc.model_gen.complexation_option (module) h1_hesc.model_gen.core (module) h1_hesc.model_gen.initialize_model_option (module) h1_hesc.model_gen.main (module) h1_hesc.model_gen.metabolism_option (module) h1_hesc.model_gen.protein_degradation_option (module) h1_hesc.model_gen.rna_degradation_option (module) h1_hesc.model_gen.transcription_option (module) h1_hesc.model_gen.translation_translocation_option (module) h1_hesc.model_sim (module) h1_hesc.model_sim.essentiality (module) h1_hesc.model_sim.main (module) h1_hesc.scaled_down_model (module) h1_hesc.scaled_down_model.kb_core (module) h1_hesc.scaled_down_model.model_core (module) h1_hesc.scaled_down_model.sim_core (module) h1_hesc.utils (module) H1ModelGenerator (class in h1_hesc.model_gen.core) handlers (h1_hesc.__main__.App.Meta attribute) has_all_inchi_structures() (in module h1_hesc.utils)

I

InitializeModelOptionGenerator (class in h1_hesc.model_gen.initialize_model_option)

K

kb() (h1_hesc.__main__.BaseController method) KbGenerator (class in h1_hesc.kb_gen.core) (class in h1_hesc.scaled_down_model.kb_core)

knowledge_base (h1_hesc.model_gen.core.OptionComponentGenerator attribute) (h1_hesc.model_gen.core.OptionGenerator attribute) (h1_hesc.model_gen.core.SubmodelOptionComponentGenerator attribute)

L

label (h1_hesc.__main__.App.Meta attribute) (h1_hesc.__main__.BaseController.Meta attribute)

M

main() (in module h1_hesc.__main__) (in module h1_hesc.kb_gen.core) (in module h1_hesc.model_gen.main) (in module h1_hesc.scaled_down_model.kb_core) (in module h1_hesc.scaled_down_model.model_core) (in module h1_hesc.scaled_down_model.sim_core)

MetabolicNetworkGenerator (class in h1_hesc.kb_gen.metabolic_network) MetabolicReactionKineticsGenerator (class in h1_hesc.kb_gen.metabolic_reaction_kinetics) MetabolismOptionGenerator (class in h1_hesc.model_gen.metabolism_option) MetabolitesGenerator (class in h1_hesc.kb_gen.metabolites) model() (h1_hesc.__main__.BaseController method)

O

option_generators (h1_hesc.model_gen.core.OptionGenerator attribute) OptionComponentGenerator (class in h1_hesc.model_gen.core) OptionGenerator (class in h1_hesc.model_gen.core)

options (h1_hesc.model_gen.core.OptionComponentGenerator attribute) (h1_hesc.model_gen.core.OptionGenerator attribute) (h1_hesc.model_gen.core.SubmodelOptionComponentGenerator attribute)

P

parse_cobra_reaction_equation() (in module h1_hesc.utils) parse_cobra_reaction_equation_side() (in module h1_hesc.utils) plot_time_series() (in module h1_hesc.model_sim.essentiality) prepare_conv_model() (in module h1_hesc.model_sim.essentiality) process_data() (h1_hesc.kb_gen.chromosomes.ChromosomesGenerator method) (h1_hesc.kb_gen.complexes.ComplexesGenerator method) (h1_hesc.kb_gen.genes_transcripts_exons_proteins.GenesTranscriptsExonsProteinsGenerator method) (h1_hesc.kb_gen.metabolic_reaction_kinetics.MetabolicReactionKineticsGenerator method) (h1_hesc.kb_gen.metabolites.MetabolitesGenerator method) (h1_hesc.kb_gen.properties.PropertiesGenerator method) (h1_hesc.kb_gen.protein_modifications.ProteinModificationsGenerator method) (h1_hesc.kb_gen.proteins.ProteinsGenerator method) (h1_hesc.kb_gen.regulatory_modules.RegulatoryModulesGenerator method) (h1_hesc.kb_gen.transcripts.TranscriptsGenerator method) (h1_hesc.model_gen.complexation_option.ComplexationOptionGenerator method) (h1_hesc.model_gen.core.SubmodelOptionComponentGenerator method) (h1_hesc.model_gen.initialize_model_option.InitializeModelOptionGenerator method) (h1_hesc.model_gen.metabolism_option.MetabolismOptionGenerator method) (h1_hesc.model_gen.protein_degradation_option.ProteinDegradationOptionGenerator method) (h1_hesc.model_gen.rna_degradation_option.RnaDegradationOptionGenerator method) (h1_hesc.model_gen.transcription_option.TranscriptionOptionGenerator method) (h1_hesc.model_gen.translation_translocation_option.TranslationTranslocationOptionGenerator method)

PropertiesGenerator (class in h1_hesc.kb_gen.properties) ProteinDegradationOptionGenerator (class in h1_hesc.model_gen.protein_degradation_option) ProteinModificationsGenerator (class in h1_hesc.kb_gen.protein_modifications) ProteinsGenerator (class in h1_hesc.kb_gen.proteins)

R

recal() (h1_hesc.__main__.BaseController method) recalibrate_initial_values() (in module h1_hesc.model_sim.essentiality) RegulatoryModulesGenerator (class in h1_hesc.kb_gen.regulatory_modules) remove_inchi_layer() (in module h1_hesc.utils) RnaDegradationOptionGenerator (class in h1_hesc.model_gen.rna_degradation_option) run() (h1_hesc.kb_gen.core.KbGenerator method) (h1_hesc.model_gen.core.OptionComponentGenerator method) (h1_hesc.model_gen.core.OptionGenerator method) (h1_hesc.model_gen.core.SubmodelOptionComponentGenerator method) (h1_hesc.scaled_down_model.kb_core.KbGenerator method)

run_essentiality() (in module h1_hesc.model_sim.essentiality) run_gene_expression() (in module h1_hesc.model_sim.essentiality)

S

sd_kb() (h1_hesc.__main__.BaseController method) sd_model() (h1_hesc.__main__.BaseController method) sd_sim() (h1_hesc.__main__.BaseController method) sim() (h1_hesc.__main__.BaseController method)

sim_main() (in module h1_hesc.model_sim.main) simulate_effect_on_growth() (in module h1_hesc.model_sim.essentiality) simulate_gene_expression() (in module h1_hesc.model_sim.essentiality) SubmodelOptionComponentGenerator (class in h1_hesc.model_gen.core)

T

TaxonGenerator (class in h1_hesc.kb_gen.taxon) TranscriptionOptionGenerator (class in h1_hesc.model_gen.transcription_option)

TranscriptsGenerator (class in h1_hesc.kb_gen.transcripts) TranslationTranslocationOptionGenerator (class in h1_hesc.model_gen.translation_translocation_option)