Index

A

add_compartment_structure_specs() (in module refinegems.polish) add_cv_term_genes() (in module refinegems.cvterms) add_cv_term_metabolites() (in module refinegems.cvterms) add_cv_term_pathways() (in module refinegems.cvterms) add_cv_term_pathways_to_entity() (in module refinegems.cvterms) add_cv_term_reactions() (in module refinegems.cvterms) add_cv_term_units() (in module refinegems.cvterms) add_fba_units() (in module refinegems.polish) add_kegg_pathways() (in module refinegems.pathways) add_metab() (in module refinegems.polish)

add_reac() (in module refinegems.polish) add_reactions_from_table() (in module refinegems.curate) add_uri_set() (in module refinegems.polish) addSBOforCompartments() (in module refinegems.sboann) addSBOforGenes() (in module refinegems.sboann) addSBOforGroups() (in module refinegems.sboann) addSBOforMetabolites() (in module refinegems.sboann) addSBOforModel() (in module refinegems.sboann) addSBOforParameters() (in module refinegems.sboann) addSBOfromDB() (in module refinegems.sboann) addSBOviaEC() (in module refinegems.sboann)

C

change_all_qualifiers() (in module refinegems.polish) change_qualifier_per_entity() (in module refinegems.polish) change_qualifiers() (in module refinegems.polish) check_normalise_biomass() (in module refinegems.biomass) checkAcetylationViaEC() (in module refinegems.sboann) checkActiveTransport() (in module refinegems.sboann) checkBiomass() (in module refinegems.sboann) checkCoTransport() (in module refinegems.sboann) checkDeamination() (in module refinegems.sboann) checkDeaminationViaEC() (in module refinegems.sboann) checkDecarbonylation() (in module refinegems.sboann) checkDecarboxylation() (in module refinegems.sboann) checkDecarboxylationViaEC() (in module refinegems.sboann) checkDemand() (in module refinegems.sboann) checkExchange() (in module refinegems.sboann) checkGlycosylation() (in module refinegems.sboann) checkGlycosylationViaEC() (in module refinegems.sboann) checkHydrolysisViaEC() (in module refinegems.sboann)

checkIsomerisationViaEC() (in module refinegems.sboann) checkMethylationViaEC() (in module refinegems.sboann) checkPassiveTransport() (in module refinegems.sboann) checkPhosphorylation() (in module refinegems.sboann) checkRedox() (in module refinegems.sboann) checkRedoxViaEC() (in module refinegems.sboann) checkSink() (in module refinegems.sboann) checkTransaminationViaEC() (in module refinegems.sboann) compare_model_modelseed() (in module refinegems.modelseed) compare_to_modelseed() (in module refinegems.modelseed) correct_charges_from_db() (in module refinegems.charges) correct_charges_modelseed() (in module refinegems.charges) create_fba_units() (in module refinegems.polish) create_pathway_groups() (in module refinegems.pathways) create_unit() (in module refinegems.polish) create_unit_definition() (in module refinegems.polish) cv_ncbiprotein() (in module refinegems.polish) cv_notes_metab() (in module refinegems.polish) cv_notes_reac() (in module refinegems.polish)

E

extract_kegg_pathways() (in module refinegems.pathways)

extract_kegg_reactions() (in module refinegems.pathways)

F

find_additives() (in module refinegems.growth)

find_minimum_essential() (in module refinegems.growth) find_missing_essential() (in module refinegems.growth)

G

gap_analysis() (in module refinegems.gapfill) gapfill() (in module refinegems.gapfill) gapfill_model() (in module refinegems.gapfill) generate_cvterm() (in module refinegems.cvterms) generate_miriam_compliant_uri_set() (in module refinegems.polish) generate_uri_set_with_specific_pattern() (in module refinegems.polish) get_all_minimum_essential() (in module refinegems.growth) get_charge_mismatch() (in module refinegems.modelseed) get_compared_formulae() (in module refinegems.modelseed) get_default_secretion() (in module refinegems.growth) get_default_uptake() (in module refinegems.growth) get_egc() (in module refinegems.investigate) get_essential_reactions() (in module refinegems.growth) get_essential_reactions_via_bounds() (in module refinegems.growth) get_formula_mismatch() (in module refinegems.modelseed) get_growth_selected_media() (in module refinegems.growth) get_id_from_cv_term() (in module refinegems.cvterms) get_mass_charge_unbalanced() (in module refinegems.investigate) get_memote_score() (in module refinegems.investigate) get_metabs_with_one_cvterm() (in module refinegems.investigate) get_minimal_uptake() (in module refinegems.growth) get_missing_exchanges() (in module refinegems.growth) get_model_charges() (in module refinegems.modelseed)

get_model_info() (in module refinegems.investigate) get_modelseed_charges() (in module refinegems.modelseed) get_modelseed_compounds() (in module refinegems.modelseed) get_orphans_deadends_disconnected() (in module refinegems.investigate) get_pathway_groups() (in module refinegems.pathways) get_reactions_per_sbo() (in module refinegems.investigate) get_sbo_mapping_multiple() (in module refinegems.comparison) get_set_of_curies() (in module refinegems.polish) getCompartmentDict() (in module refinegems.sboann) getCompartmentFromSpeciesRef() (in module refinegems.sboann) getCompartmentlessMetaboliteIds() (in module refinegems.sboann) getCompartmentlessProductIds() (in module refinegems.sboann) getCompartmentlessReactantIds() (in module refinegems.sboann) getCompartmentlessSpeciesId() (in module refinegems.sboann) getCompartmentList() (in module refinegems.sboann) getECNums() (in module refinegems.sboann) getListOfMetabolites() (in module refinegems.sboann) getMetaboliteIds() (in module refinegems.sboann) getProductCompartmentList() (in module refinegems.sboann) getProductIds() (in module refinegems.sboann) getReactantCompartmentList() (in module refinegems.sboann) getReactantIds() (in module refinegems.sboann) growth_one_medium_from_default() (in module refinegems.growth) growth_one_medium_from_minimal() (in module refinegems.growth)

H

hasReactantPair() (in module refinegems.sboann)

I

improve_uri_per_entity() (in module refinegems.polish) improve_uris() (in module refinegems.polish)

initial_analysis() (in module refinegems.investigate) isProtonTransport() (in module refinegems.sboann)

K

kegg_pathways() (in module refinegems.pathways)

L

load_a_table_from_database() (in module refinegems.io) load_all_media_from_db() (in module refinegems.io) load_document_libsbml() (in module refinegems.io) load_manual_annotations() (in module refinegems.io) load_manual_gapfill() (in module refinegems.io)

load_medium_custom() (in module refinegems.io) load_medium_from_db() (in module refinegems.io) load_model_cobra() (in module refinegems.io) load_model_enable_groups() (in module refinegems.pathways) load_model_libsbml() (in module refinegems.io) load_multiple_models() (in module refinegems.io)

M

modify_medium() (in module refinegems.growth) module refinegems.biomass refinegems.charges refinegems.comparison refinegems.curate refinegems.cvterms refinegems.gapfill refinegems.growth refinegems.investigate refinegems.io refinegems.modelseed refinegems.pathways refinegems.polish refinegems.sboann

moreThanTwoCompartmentTransport() (in module refinegems.sboann)

N

normalise_biomass() (in module refinegems.biomass)

P

parse_dict_to_dataframe() (in module refinegems.io) parse_fasta_headers() (in module refinegems.io) parse_gff_for_gp_info() (in module refinegems.io) parse_reaction() (in module refinegems.investigate) plot_heatmap_dt() (in module refinegems.comparison) plot_heatmap_native() (in module refinegems.comparison) plot_initial_analysis() (in module refinegems.comparison) plot_rea_sbo_multiple() (in module refinegems.comparison)

plot_rea_sbo_single() (in module refinegems.investigate) plot_venn() (in module refinegems.comparison) polish() (in module refinegems.polish) polish_annotations() (in module refinegems.polish) polish_entities() (in module refinegems.polish) print_cvterm() (in module refinegems.cvterms) print_remaining_UnitDefinitions() (in module refinegems.polish) print_UnitDefinitions() (in module refinegems.polish)

R

refinegems.biomass module refinegems.charges module refinegems.comparison module refinegems.curate module refinegems.cvterms module refinegems.gapfill module refinegems.growth module

refinegems.investigate module refinegems.io module refinegems.modelseed module refinegems.pathways module refinegems.polish module refinegems.sboann module returnCompartment() (in module refinegems.sboann) run_memote() (in module refinegems.investigate) run_memote_sys() (in module refinegems.investigate)

S

save_user_input() (in module refinegems.io) sbo_annotation() (in module refinegems.sboann) search_ncbi_for_gpr() (in module refinegems.io) search_sbo_label() (in module refinegems.io) set_default_units() (in module refinegems.polish) set_fluxes_to_simulate() (in module refinegems.growth) set_initial_amount() (in module refinegems.polish)

set_units() (in module refinegems.polish) simulate_all() (in module refinegems.comparison) simulate_minimum_essential() (in module refinegems.growth) soleProtonTransported() (in module refinegems.sboann) splitSymAntiPorter() (in module refinegems.sboann) splitTransportBiochem() (in module refinegems.sboann) sum_biomass_weight() (in module refinegems.biomass)

T

test_biomass_consistency() (in module refinegems.biomass)

test_biomass_presence() (in module refinegems.biomass)

U

update_annotations_from_others() (in module refinegems.curate)

update_annotations_from_table() (in module refinegems.curate)

V

validate_libsbml_model() (in module refinegems.io)

W

write_report() (in module refinegems.io)

write_to_file() (in module refinegems.io)