Index

A

add_compartment() (set_up_grasp_models.model.model.Model method) add_metabolite() (set_up_grasp_models.model.model.Model method)

add_reaction() (set_up_grasp_models.model.model.Model method) add_reaction_from_str() (set_up_grasp_models.model.model.Model method) AttrOrderedDict (class in set_up_grasp_models.model.model)

C

calculate_dG() (in module set_up_grasp_models.check_models.thermodynamics_checks) check_balanced_metabolites() (in module set_up_grasp_models.check_models.mass_balance_checks) check_flux_balance() (in module set_up_grasp_models.check_models.mass_balance_checks) check_kinetics_met_separators() (in module set_up_grasp_models.check_models.format_checks) check_kinetics_subs_prod_order() (in module set_up_grasp_models.check_models.format_checks) check_met_rxn_order() (in module set_up_grasp_models.check_models.format_checks)

check_rxn_mechanism_order() (in module set_up_grasp_models.check_models.format_checks) check_thermodynamic_feasibility() (in module set_up_grasp_models.check_models.thermodynamics_checks) Compartment (class in set_up_grasp_models.model.model) convert_er_mech_to_grasp_pattern() (in module set_up_grasp_models.set_up_models.convert_mechanisms) convert_rxns_to_kegg() (in module set_up_grasp_models.set_up_models.set_up_thermo_rxns) copy() (set_up_grasp_models.model.model.Model method)

G

generate_mechanisms() (in module set_up_grasp_models.set_up_models.convert_mechanisms) get_activators() (set_up_grasp_models.model.model.Reaction method) get_boundary_metabolites() (set_up_grasp_models.model.model.Model method) get_dGs() (in module set_up_grasp_models.set_up_models.set_up_thermo_rxns) get_exchange_reactions() (set_up_grasp_models.model.model.Model method) get_inhibitors() (set_up_grasp_models.model.model.Reaction method) get_metabolite_consumers() (set_up_grasp_models.model.model.Model method)

get_metabolite_producers() (set_up_grasp_models.model.model.Model method) get_metabolite_reactions() (set_up_grasp_models.model.model.Model method) get_metabolites_by_compartment() (set_up_grasp_models.model.model.Model method) get_products() (set_up_grasp_models.model.model.Reaction method) get_robust_fluxes() (in module set_up_grasp_models.check_models.thermodynamics_checks) get_sink_reactions() (set_up_grasp_models.model.model.Model method) get_stoic() (in module set_up_grasp_models.set_up_models.set_up_model) get_substrates() (set_up_grasp_models.model.model.Reaction method)

I

import_model_from_plaintext() (in module set_up_grasp_models.io.plaintext)

import_stoic() (in module set_up_grasp_models.io.stoic)

M

Metabolite (class in set_up_grasp_models.model.model) metabolite_reaction_lookup() (set_up_grasp_models.model.model.Model method) Model (class in set_up_grasp_models.model.model) module set_up_grasp_models.check_models.format_checks set_up_grasp_models.check_models.mass_balance_checks set_up_grasp_models.check_models.thermodynamics_checks set_up_grasp_models.io.plaintext set_up_grasp_models.io.stoic set_up_grasp_models.model.model set_up_grasp_models.model.parser set_up_grasp_models.set_up_models.convert_mechanisms set_up_grasp_models.set_up_models.set_up_model set_up_grasp_models.set_up_models.set_up_thermo_rxns

P

print_reaction() (set_up_grasp_models.model.model.Model method)

R

Reaction (class in set_up_grasp_models.model.model) remove_compartment() (set_up_grasp_models.model.model.Model method) remove_compartments() (set_up_grasp_models.model.model.Model method) remove_metabolite() (set_up_grasp_models.model.model.Model method) remove_metabolites() (set_up_grasp_models.model.model.Model method)

remove_reaction() (set_up_grasp_models.model.model.Model method) remove_reactions() (set_up_grasp_models.model.model.Model method) remove_spaces() (in module set_up_grasp_models.set_up_models.manipulate_model) rename_columns() (in module set_up_grasp_models.set_up_models.manipulate_model) reorder_reactions() (in module set_up_grasp_models.set_up_models.manipulate_model)

S

set_up_grasp_models.check_models.format_checks module set_up_grasp_models.check_models.mass_balance_checks module set_up_grasp_models.check_models.thermodynamics_checks module set_up_grasp_models.io.plaintext module set_up_grasp_models.io.stoic module set_up_grasp_models.model.model module

set_up_grasp_models.model.parser module set_up_grasp_models.set_up_models.convert_mechanisms module set_up_grasp_models.set_up_models.set_up_model module set_up_grasp_models.set_up_models.set_up_thermo_rxns module set_up_model() (in module set_up_grasp_models.set_up_models.set_up_model) stoichiometric_matrix() (set_up_grasp_models.model.model.Model method)

T

to_equation_string() (set_up_grasp_models.model.model.Reaction method)

to_string() (set_up_grasp_models.model.model.Model method) (set_up_grasp_models.model.model.Reaction method)

U

update_stoic() (in module set_up_grasp_models.set_up_models.set_up_model)

W

write_to_plaintext() (in module set_up_grasp_models.io.plaintext)