Index

A

abundance (equilibrator_api.phased_compound.Condition property) (equilibrator_api.phased_compound.PhasedCompound property) (equilibrator_api.phased_compound.Proton property)

add_stoichiometry() (equilibrator_api.phased_reaction.PhasedReaction method) AQUEOUS_PHASE_NAME (in module equilibrator_api.phased_compound) atom_bag (equilibrator_api.phased_compound.PhasedCompound property) (equilibrator_api.phased_compound.RedoxCarrier property)

B

balance_by_oxidation() (equilibrator_api.component_contribution.ComponentContribution method) BaseBounds (class in equilibrator_api.model.bounds)

bound_df (equilibrator_api.model.model.StoichiometricModel property) Bounds (class in equilibrator_api.model.bounds) bounds (equilibrator_api.model.model.StoichiometricModel property)

C

CARBONATE_INCHIS (in module equilibrator_api.phased_compound) check_bounds() (equilibrator_api.model.bounds.Bounds method) clone() (equilibrator_api.phased_reaction.PhasedReaction method) ComponentContribution (class in equilibrator_api.component_contribution) compound_df (equilibrator_api.model.model.StoichiometricModel property) compound_ids (equilibrator_api.model.model.StoichiometricModel property) compounds (equilibrator_api.model.model.StoichiometricModel property)

conc2ln_conc() (equilibrator_api.model.bounds.BaseBounds static method) Condition (class in equilibrator_api.phased_compound) configure() (equilibrator_api.model.model.StoichiometricModel method) copy() (equilibrator_api.model.bounds.BaseBounds method) (equilibrator_api.model.bounds.Bounds method) create_stoichiometric_matrix_from_reaction_formulas() (equilibrator_api.component_contribution.ComponentContribution static method) create_stoichiometric_matrix_from_reaction_objects() (equilibrator_api.component_contribution.ComponentContribution method)

D

DEFAULT_BOUNDS (equilibrator_api.model.bounds.Bounds attribute) default_conc_lb (in module equilibrator_api) default_conc_ub (in module equilibrator_api) default_e_potential (in module equilibrator_api) default_phase (in module equilibrator_api) default_physiological_ionic_strength (in module equilibrator_api) default_physiological_p_h (in module equilibrator_api) default_physiological_p_mg (in module equilibrator_api)

default_physiological_temperature (in module equilibrator_api) default_rmse_inf (in module equilibrator_api) dg_analysis() (equilibrator_api.component_contribution.ComponentContribution method) dg_correction() (equilibrator_api.phased_reaction.PhasedReaction method) dg_prime() (equilibrator_api.component_contribution.ComponentContribution method) dg_prime_sensitivity_to_p_h() (equilibrator_api.component_contribution.ComponentContribution method) dgf_prime_sensitivity_to_p_h() (equilibrator_api.component_contribution.ComponentContribution method) dimensionality (equilibrator_api.phased_compound.Condition property)

E

e_prime() (equilibrator_api.component_contribution.ComponentContribution method) equilibrator_api module equilibrator_api.compatibility module equilibrator_api.component_contribution module equilibrator_api.data module equilibrator_api.model module

equilibrator_api.model.bounds module equilibrator_api.model.model module equilibrator_api.phased_compound module equilibrator_api.phased_reaction module equilibrator_api.reaction_parser module

F

find_most_abundant_ms() (in module equilibrator_api.component_contribution) formula (equilibrator_api.phased_compound.PhasedCompound property)

from_csv() (equilibrator_api.model.bounds.Bounds class method) from_network_sbtab() (equilibrator_api.model.model.StoichiometricModel class method) from_sbtab() (equilibrator_api.model.model.StoichiometricModel class method)

G

GAS_PHASE_NAME (in module equilibrator_api.phased_compound) get_abundance() (equilibrator_api.phased_reaction.PhasedReaction method) get_bound_tuple() (equilibrator_api.model.bounds.BaseBounds method) get_bounds() (equilibrator_api.model.bounds.BaseBounds method) (equilibrator_api.model.model.StoichiometricModel method) get_compound() (equilibrator_api.component_contribution.ComponentContribution method) get_compound_by_inchi() (equilibrator_api.component_contribution.ComponentContribution method) get_default_bounds() (equilibrator_api.model.bounds.Bounds static method) get_element_data_frame() (equilibrator_api.phased_reaction.PhasedReaction method) get_ln_bounds() (equilibrator_api.model.bounds.BaseBounds method) get_ln_lower_bounds() (equilibrator_api.model.bounds.BaseBounds method) get_ln_upper_bounds() (equilibrator_api.model.bounds.BaseBounds method) get_lower_bound() (equilibrator_api.model.bounds.BaseBounds method) (equilibrator_api.model.bounds.Bounds method)

get_lower_bounds() (equilibrator_api.model.bounds.BaseBounds method) get_oxidation_reaction() (equilibrator_api.component_contribution.ComponentContribution method) get_phase() (equilibrator_api.phased_reaction.PhasedReaction method) get_phased_compound() (equilibrator_api.phased_reaction.PhasedReaction method) get_stoichiometry() (equilibrator_api.phased_reaction.PhasedReaction method) get_stored_microspecie() (equilibrator_api.phased_compound.PhasedCompound method) get_stored_standard_dgf() (equilibrator_api.phased_compound.PhasedCompound method) (equilibrator_api.phased_compound.RedoxCarrier method) get_stored_standard_dgf_prime() (equilibrator_api.phased_compound.PhasedCompound method) (equilibrator_api.phased_compound.RedoxCarrier method) get_upper_bound() (equilibrator_api.model.bounds.BaseBounds method) (equilibrator_api.model.bounds.Bounds method) get_upper_bounds() (equilibrator_api.model.bounds.BaseBounds method)

H

hash_md5() (equilibrator_api.phased_reaction.PhasedReaction method)

html_formula (equilibrator_api.phased_compound.PhasedCompound property)

I

id (equilibrator_api.phased_compound.PhasedCompound property) inchi (equilibrator_api.phased_compound.PhasedCompound property) inchi_key (equilibrator_api.phased_compound.PhasedCompound property) initialize_custom_version() (equilibrator_api.component_contribution.ComponentContribution static method) ionic_strength (equilibrator_api.component_contribution.ComponentContribution property)

is_physiological (equilibrator_api.phased_compound.Condition property) (equilibrator_api.phased_compound.PhasedCompound property) (equilibrator_api.phased_compound.RedoxCarrier property) (equilibrator_api.phased_reaction.PhasedReaction property) is_using_group_contribution() (equilibrator_api.component_contribution.ComponentContribution method)

L

legacy() (equilibrator_api.component_contribution.ComponentContribution static method) LIQUID_PHASE_NAME (in module equilibrator_api.phased_compound) ln_abundance (equilibrator_api.phased_compound.Condition property) (equilibrator_api.phased_compound.PhasedCompound property) (equilibrator_api.phased_compound.Proton property) (equilibrator_api.phased_compound.RedoxCarrier property) ln_conc_lb (equilibrator_api.model.model.StoichiometricModel property)

ln_conc_mu (equilibrator_api.model.model.StoichiometricModel property) ln_conc_sigma (equilibrator_api.model.model.StoichiometricModel property) ln_conc_ub (equilibrator_api.model.model.StoichiometricModel property) ln_physiological_abundance (equilibrator_api.phased_compound.Condition property) (equilibrator_api.phased_compound.PhasedCompound property) (equilibrator_api.phased_compound.Proton property) (equilibrator_api.phased_compound.RedoxCarrier property) ln_reversibility_index() (equilibrator_api.component_contribution.ComponentContribution method)

M

make_reaction_parser() (in module equilibrator_api.reaction_parser) map_cobra_reactions() (in module equilibrator_api.compatibility) mass (equilibrator_api.phased_compound.PhasedCompound property) MicroSpecie (in module equilibrator_api.phased_compound) MINIMAL_STDEV (equilibrator_api.model.model.StoichiometricModel attribute) module equilibrator_api equilibrator_api.compatibility equilibrator_api.component_contribution equilibrator_api.data equilibrator_api.model equilibrator_api.model.bounds equilibrator_api.model.model equilibrator_api.phased_compound equilibrator_api.phased_reaction equilibrator_api.reaction_parser

multicompartmental_standard_dg_prime() (equilibrator_api.component_contribution.ComponentContribution method)

N

NON_AQUEOUS_COMPOUND_DICT (in module equilibrator_api.phased_compound)

O

open_sbtabdoc() (in module equilibrator_api.model)

P

p_h (equilibrator_api.component_contribution.ComponentContribution property) p_mg (equilibrator_api.component_contribution.ComponentContribution property) parse_formula() (equilibrator_api.component_contribution.ComponentContribution static method) parse_formula_side() (equilibrator_api.component_contribution.ComponentContribution static method) parse_reaction_formula() (equilibrator_api.component_contribution.ComponentContribution method) phase (equilibrator_api.phased_compound.Condition property) (equilibrator_api.phased_compound.PhasedCompound property) PHASE_INFO_DICT (in module equilibrator_api.phased_compound) phase_shorthand (equilibrator_api.phased_compound.PhasedCompound property) PHASED_COMPOUND_DICT (in module equilibrator_api.phased_compound)

PhasedCompound (class in equilibrator_api.phased_compound) PhasedReaction (class in equilibrator_api.phased_reaction) PhaseInfo (in module equilibrator_api.phased_compound) physiolical_abundance (equilibrator_api.phased_compound.Condition property) physiological_dg_correction() (equilibrator_api.phased_reaction.PhasedReaction method) physiological_dg_prime() (equilibrator_api.component_contribution.ComponentContribution method) physiological_e_prime() (equilibrator_api.component_contribution.ComponentContribution method) possible_phases (equilibrator_api.phased_compound.PhasedCompound property) POSSIBLE_REACTION_ARROWS (in module equilibrator_api.reaction_parser) predict_protons_and_charge() (in module equilibrator_api.component_contribution) Proton (class in equilibrator_api.phased_compound)

R

REACTION_COUNTER (equilibrator_api.phased_reaction.PhasedReaction attribute) reaction_df (equilibrator_api.model.model.StoichiometricModel property) reaction_formulas (equilibrator_api.model.model.StoichiometricModel property) reaction_ids (equilibrator_api.model.model.StoichiometricModel property) reactions (equilibrator_api.model.model.StoichiometricModel property) read_thermodynamics() (equilibrator_api.model.model.StoichiometricModel static method)

REDOX_PHASE_NAME (in module equilibrator_api.phased_compound) RedoxCarrier (class in equilibrator_api.phased_compound) reset_abundance() (equilibrator_api.phased_compound.Condition method) (equilibrator_api.phased_compound.PhasedCompound method) reset_abundances() (equilibrator_api.phased_reaction.PhasedReaction method) reverse() (equilibrator_api.phased_reaction.PhasedReaction method) RT (equilibrator_api.component_contribution.ComponentContribution property)

S

search_compound() (equilibrator_api.component_contribution.ComponentContribution method) search_compound_by_inchi_key() (equilibrator_api.component_contribution.ComponentContribution method) search_reaction() (equilibrator_api.component_contribution.ComponentContribution method) separate_stored_dg() (equilibrator_api.phased_reaction.PhasedReaction method) separate_stored_dg_prime() (equilibrator_api.phased_reaction.PhasedReaction method) serialize() (equilibrator_api.phased_compound.PhasedCompound method) (equilibrator_api.phased_reaction.PhasedReaction method) set_abundance() (equilibrator_api.phased_reaction.PhasedReaction method) set_bounds() (equilibrator_api.model.bounds.BaseBounds method) (equilibrator_api.model.model.StoichiometricModel method)

set_phase() (equilibrator_api.phased_reaction.PhasedReaction method) smiles (equilibrator_api.phased_compound.PhasedCompound property) SOLID_PHASE_NAME (in module equilibrator_api.phased_compound) standard_abundance (equilibrator_api.phased_compound.Condition property) standard_dg() (equilibrator_api.component_contribution.ComponentContribution method) standard_dg_formation() (equilibrator_api.component_contribution.ComponentContribution method) standard_dg_multi() (equilibrator_api.component_contribution.ComponentContribution method) standard_dg_prime() (equilibrator_api.component_contribution.ComponentContribution method) standard_dg_prime_multi() (equilibrator_api.component_contribution.ComponentContribution method) standard_e_prime() (equilibrator_api.component_contribution.ComponentContribution method) StoichiometricModel (class in equilibrator_api.model.model)

T

temperature (equilibrator_api.component_contribution.ComponentContribution property) to_data_frame() (equilibrator_api.model.bounds.Bounds method)

to_phased_compound() (equilibrator_api.phased_reaction.PhasedReaction static method) to_sbtab() (equilibrator_api.model.model.StoichiometricModel method)

U

update_standard_dgs() (equilibrator_api.model.model.StoichiometricModel method)

W

write_sbtab() (equilibrator_api.model.model.StoichiometricModel method)