Index

A

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_kegg_pathways() (in module refinegems.pathways) add_reactions_from_table() (in module refinegems.curate)

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

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_pathway_groups() (in module refinegems.pathways)

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

generate_cvterm() (in module refinegems.cvterms) 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_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_minimal_uptake() (in module refinegems.growth) get_missing_exchanges() (in module refinegems.growth) get_model_charges() (in module refinegems.modelseed) get_modelseed_charges() (in module refinegems.modelseed) get_modelseed_compounds() (in module refinegems.modelseed)

get_pathway_groups() (in module refinegems.pathways) 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

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.charges refinegems.curate refinegems.cvterms refinegems.growth refinegems.io refinegems.modelseed refinegems.pathways refinegems.sboann

moreThanTwoCompartmentTransport() (in module refinegems.sboann)

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) print_cvterm() (in module refinegems.cvterms)

R

refinegems.charges module refinegems.curate module refinegems.cvterms module refinegems.growth module

refinegems.io module refinegems.modelseed module refinegems.pathways module refinegems.sboann module returnCompartment() (in module refinegems.sboann)

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_fluxes_to_simulate() (in module refinegems.growth) simulate_minimum_essential() (in module refinegems.growth) soleProtonTransported() (in module refinegems.sboann) splitSymAntiPorter() (in module refinegems.sboann) splitTransportBiochem() (in module refinegems.sboann)

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)