Index

A

add_a_peg() (PyFBA.metabolism.Enzyme method) add_enzymes() (PyFBA.metabolism.Reaction method) add_left_compounds() (PyFBA.metabolism.Reaction method) add_pegs() (PyFBA.metabolism.Enzyme method) (PyFBA.metabolism.Reaction method) add_reaction() (PyFBA.metabolism.Enzyme method) add_reactions() (PyFBA.metabolism.Compound method)

add_right_compounds() (PyFBA.metabolism.Reaction method) add_roles() (PyFBA.metabolism.Enzyme method) all_compounds() (PyFBA.metabolism.Reaction method) all_enzymes() (PyFBA.metabolism.Reaction method) all_reactions() (PyFBA.metabolism.Compound method)

C

calculate_molecular_weight() (PyFBA.metabolism.Compound method) check_input_output() (PyFBA.metabolism.Reaction method) Compound (class in PyFBA.metabolism)

compound_bounds() (in module PyFBA.fba.bounds) compound_probability() (in module PyFBA.gapfill.probability) create_stoichiometric_matrix() (in module PyFBA.fba.create_stoichiometric_matrix)

E

Enzyme (class in PyFBA.metabolism)

G

get_deltaG() (PyFBA.metabolism.Reaction method) get_left_compound_abundance() (PyFBA.metabolism.Reaction method) get_probability_left_to_right() (PyFBA.metabolism.Reaction method)

get_probability_right_to_left() (PyFBA.metabolism.Reaction method) get_right_compound_abundance() (PyFBA.metabolism.Reaction method)

H

has() (PyFBA.metabolism.Reaction method) has_enzyme() (PyFBA.metabolism.Reaction method) has_peg() (PyFBA.metabolism.Reaction method)

has_peg_for_role() (PyFBA.metabolism.Enzyme method) has_reaction() (PyFBA.metabolism.Compound method) has_role() (PyFBA.metabolism.Enzyme method)

I

is_common() (PyFBA.metabolism.Compound method) is_input_reaction() (PyFBA.metabolism.Reaction method)

is_output_reaction() (PyFBA.metabolism.Reaction method)

N

number_of_compounds() (PyFBA.metabolism.Reaction method) number_of_enzymes() (PyFBA.metabolism.Reaction method) number_of_left_compounds() (PyFBA.metabolism.Reaction method) number_of_pegs() (PyFBA.metabolism.Enzyme method)

number_of_reactions() (PyFBA.metabolism.Compound method) (PyFBA.metabolism.Enzyme method) number_of_right_compounds() (PyFBA.metabolism.Reaction method) number_of_roles() (PyFBA.metabolism.Enzyme method) number_of_roles_with_pegs() (PyFBA.metabolism.Enzyme method)

O

opposite_sides() (PyFBA.metabolism.Reaction method)

P

probability() (PyFBA.metabolism.Enzyme method) PyFBA (module) PyFBA.fba.bounds (module) PyFBA.fba.create_stoichiometric_matrix (module) PyFBA.fba.external_reactions (module) PyFBA.fba.run_fba (module) PyFBA.filters.reactions_and_proteins (module) PyFBA.filters.roles_and_reactions (module)

PyFBA.gapfill.essentials (module) PyFBA.gapfill.maps_to_proteins (module) PyFBA.gapfill.media (module) PyFBA.gapfill.orphan_compound (module) PyFBA.gapfill.probability (module) PyFBA.gapfill.roles (module) PyFBA.gapfill.subsystem (module) PyFBA.parse (module)

R

Reaction (class in PyFBA.metabolism) reaction_bounds() (in module PyFBA.fba.bounds) reactions_to_roles() (in module PyFBA.filters.roles_and_reactions) reactions_with_no_proteins() (in module PyFBA.filters.reactions_and_proteins) reactions_with_proteins() (in module PyFBA.filters.reactions_and_proteins)

remove_uptake_and_secretion_reactions() (in module PyFBA.fba.external_reactions) reverse_reaction() (PyFBA.metabolism.Reaction method) roles_to_reactions() (in module PyFBA.filters.roles_and_reactions) run_fba() (in module PyFBA.fba.run_fba)

S

set_deltaG() (PyFBA.metabolism.Reaction method) set_direction() (PyFBA.metabolism.Reaction method) set_left_compound_abundance() (PyFBA.metabolism.Reaction method) set_probability_left_to_right() (PyFBA.metabolism.Reaction method) set_probability_right_to_left() (PyFBA.metabolism.Reaction method) set_right_compound_abundance() (PyFBA.metabolism.Reaction method) suggest_by_compound() (in module PyFBA.gapfill.orphan_compound)

suggest_essential_reactions() (in module PyFBA.gapfill.essentials) suggest_from_media() (in module PyFBA.gapfill.media) suggest_from_roles() (in module PyFBA.gapfill.roles) suggest_reactions_from_subsystems() (in module PyFBA.gapfill.subsystem) suggest_reactions_with_proteins() (in module PyFBA.gapfill.maps_to_proteins) suggest_reactions_without_proteins() (in module PyFBA.gapfill.maps_to_proteins)

T

toggle_input_reaction() (PyFBA.metabolism.Reaction method)

toggle_output_reaction() (PyFBA.metabolism.Reaction method)

U

uptake_and_secretion_reactions() (in module PyFBA.fba.external_reactions)