Index

A

add_boundary_metabolites_to_exchange_compartment() (pycomo.pycomo_models.SingleOrganismModel method) add_exchange_compartment() (pycomo.pycomo_models.SingleOrganismModel method) add_exchange_reactions_to_compartment() (pycomo.pycomo_models.SingleOrganismModel method) add_exchange_reactions_to_metabolites() (pycomo.pycomo_models.SingleOrganismModel method)

add_sink_reactions_to_metabolites() (pycomo.pycomo_models.CommunityModel method) apply_fixed_abundance() (pycomo.pycomo_models.CommunityModel method) apply_fixed_growth_rate() (pycomo.pycomo_models.CommunityModel method) apply_medium() (pycomo.pycomo_models.CommunityModel method)

C

change_reaction_bounds() (pycomo.pycomo_models.CommunityModel method) check_annotation_overlap_of_metabolites_with_identical_id() (in module pycomo.helper.utils) check_args() (in module pycomo.helper.cli) check_mass_balance_fomula_safe() (in module pycomo.helper.utils) check_mass_balance_of_metabolites_with_identical_id() (in module pycomo.helper.utils) check_metabolite_equal_mass() (in module pycomo.helper.utils) close_to_zero() (in module pycomo.helper.utils) CommunityModel (class in pycomo.pycomo_models) configure_logger() (in module pycomo.helper.logger) convert_constraints_to_metabolites() (pycomo.pycomo_models.CommunityModel method)

convert_exchange_to_transfer_reaction() (pycomo.pycomo_models.SingleOrganismModel method) convert_to_fixed_abundance() (pycomo.pycomo_models.CommunityModel method) convert_to_fixed_growth_rate() (pycomo.pycomo_models.CommunityModel method) convert_to_model_without_fraction_metabolites() (pycomo.pycomo_models.CommunityModel method) create_abundance_parameter() (in module pycomo.helper.utils) create_arg_parser() (in module pycomo.helper.cli) create_fraction_reaction() (pycomo.pycomo_models.CommunityModel method) create_parameter_in_sbml_model() (in module pycomo.helper.utils) cross_feeding_metabolites_from_fba() (pycomo.pycomo_models.CommunityModel method) cross_feeding_metabolites_from_fva() (pycomo.pycomo_models.CommunityModel method)

D

doall() (in module pycomo.pycomo_models)

E

ensure_compartment_suffix() (pycomo.pycomo_models.SingleOrganismModel method)

equal_abundance() (pycomo.pycomo_models.CommunityModel method)

F

f_metabolites (pycomo.pycomo_models.CommunityModel property) f_reactions (pycomo.pycomo_models.CommunityModel property) fba_solution_flux_vector() (pycomo.pycomo_models.CommunityModel method) feasible_composition_range() (pycomo.pycomo_models.CommunityModel method) filter() (pycomo.helper.logger.RegexFilter method) find_incoherent_bounds() (in module pycomo.helper.utils)

find_loops_in_model() (in module pycomo.helper.utils) find_matching_annotations() (in module pycomo.helper.utils) find_metabolites_without_exchange_rxn() (pycomo.pycomo_models.SingleOrganismModel method) force_add_exchange() (pycomo.pycomo_models.SingleOrganismModel method) format_exchg_rxns() (pycomo.pycomo_models.CommunityModel method) fva() (in module pycomo.helper.multiprocess) fva_solution_flux_vector() (pycomo.pycomo_models.CommunityModel method)

G

generate_community_model() (pycomo.pycomo_models.CommunityModel method) generate_equal_abundance_dict() (pycomo.pycomo_models.CommunityModel method) generate_member_name_conversion_dict() (pycomo.pycomo_models.CommunityModel method) get_abundance_parameters_from_sbml_doc() (in module pycomo.helper.utils) get_abundance_parameters_from_sbml_file() (in module pycomo.helper.utils) get_exchange_metabolites() (in module pycomo.helper.utils) get_f_reactions() (in module pycomo.helper.utils) get_flags_and_muc_from_sbml_file() (in module pycomo.helper.utils) get_logger_conf() (in module pycomo.helper.logger)

get_loops() (pycomo.pycomo_models.CommunityModel method) get_member_name_of_compartment() (pycomo.pycomo_models.CommunityModel method) get_member_name_of_metabolite() (pycomo.pycomo_models.CommunityModel method) get_member_name_of_reaction() (pycomo.pycomo_models.CommunityModel method) get_member_names() (pycomo.pycomo_models.CommunityModel method) get_metabolite_id_without_compartment() (in module pycomo.helper.utils) get_model_biomass_compound() (in module pycomo.helper.utils) get_name_conversion() (pycomo.pycomo_models.SingleOrganismModel method) get_unbalanced_reactions() (pycomo.pycomo_models.CommunityModel method)

H

handle_boundary_biomass_reaction() (pycomo.pycomo_models.SingleOrganismModel method)

I

is_mass_balanced() (pycomo.pycomo_models.CommunityModel method)

L

list_contains_unique_strings() (in module pycomo.helper.utils) list_of_strings_is_self_contained() (in module pycomo.helper.utils) list_without_element() (in module pycomo.helper.utils) load() (pycomo.pycomo_models.CommunityModel class method)

load_medium_from_file() (pycomo.pycomo_models.CommunityModel method) load_named_model() (in module pycomo.helper.utils) load_named_models_from_dir() (in module pycomo.helper.utils) loopless_fva() (in module pycomo.helper.multiprocess)

M

main() (in module pycomo.pycomo_models) make_model_ids_sbml_conform() (in module pycomo.helper.utils) make_string_sbml_id_compatible() (in module pycomo.helper.utils) max_growth_rate() (pycomo.pycomo_models.CommunityModel method) medium (pycomo.pycomo_models.CommunityModel property) merge_fraction_reactions() (pycomo.pycomo_models.CommunityModel method) model (pycomo.pycomo_models.CommunityModel property)

module pycomo.helper.cli pycomo.helper.logger pycomo.helper.multiprocess pycomo.helper.spawnprocesspool pycomo.helper.utils pycomo.pycomo_models

P

potential_metabolite_exchanges() (pycomo.pycomo_models.CommunityModel method) prefix_gene_names() (pycomo.pycomo_models.SingleOrganismModel method) prefix_metabolite_names() (pycomo.pycomo_models.SingleOrganismModel method) prefix_reaction_names() (pycomo.pycomo_models.SingleOrganismModel method) prepare_for_merging() (pycomo.pycomo_models.SingleOrganismModel method) pycomo.helper.cli module pycomo.helper.logger module

pycomo.helper.multiprocess module pycomo.helper.spawnprocesspool module pycomo.helper.utils module pycomo.pycomo_models module

R

read_abundance_from_file() (in module pycomo.helper.utils) read_medium_from_file() (in module pycomo.helper.utils) read_sbml_model_from_file() (in module pycomo.helper.utils) RegexFilter (class in pycomo.helper.logger) relax_reaction_constraints_for_zero_flux() (in module pycomo.helper.utils) remove_ascii_escape_from_string() (in module pycomo.helper.utils) remove_biomass_exchange_rxn() (pycomo.pycomo_models.SingleOrganismModel method)

remove_dunder_from_ascii_escape() (in module pycomo.helper.utils) rename_comp_in_met_id() (pycomo.pycomo_models.SingleOrganismModel method) rename_comp_in_rxn_id() (pycomo.pycomo_models.SingleOrganismModel method) rename_compartment() (pycomo.pycomo_models.SingleOrganismModel method) replace_metabolite_stoichiometry() (in module pycomo.helper.utils) report() (pycomo.pycomo_models.CommunityModel method) run_fba() (pycomo.pycomo_models.CommunityModel method) run_fva() (pycomo.pycomo_models.CommunityModel method)

S

save() (pycomo.pycomo_models.CommunityModel method) set_name_via_annotation() (pycomo.pycomo_models.SingleOrganismModel method)

SingleOrganismModel (class in pycomo.pycomo_models) SpawnProcessPool (class in pycomo.helper.spawnprocesspool) summary() (pycomo.pycomo_models.CommunityModel method)

T

transfer_reactions (pycomo.pycomo_models.CommunityModel property)

transport_reactions (pycomo.pycomo_models.CommunityModel property)