set_up_models
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Set up GRASP models
Check GRASP models
Misc
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set_up_models
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C
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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)