Function reference

eQuilibrator.Equilibrator — Type

struct Equilibrator

A struct used to reference the equilibrator_api object.

eq
cc

source

eQuilibrator.Equilibrator — Method

Equilibrator(; pH, pMg, ionic_strength, temperature)

A constructor for Equilibrator. Keyword arguments ionic_strength and temperature have units. Any appropriate unit may be used, the conversion is handled internally. This is typically slow to load, ~ 30 seconds, since all the thermodynamic data needs to be loaded into memory.

Example

using eQuilibrator
using Unitful

equilibrator = Equilibrator(pH=6.0, pMg = 2.5, ionic_strength=250.0u"mM", temperature=30.0u"°C")

source

eQuilibrator.get_ionic_strength — Method

get_ionic_strength(equilibrator)

Get the ionic strength of equilibrator.

Example

get_ionic_strength(equilibrator)

source

eQuilibrator.get_pH — Method

get_pH(equilibrator)

Get the pH from equilibrator.

Example

get_pH(equilibrator)

source

eQuilibrator.get_pMg — Method

get_pMg(equilibrator)

Get pMg from equilibrator.

Example

get_pMg(equilibrator)

source

eQuilibrator.get_temperature — Method

get_temperature(equilibrator)

Get the temperature of equilibrator.

Example

get_temperature(equilibrator)

source

eQuilibrator.reset_equilibrator — Method

reset_equilibrator(equilibrator)

Reset equilibrator back to the default starting state with pH = 7.5, pMg = 3.0, temperature = 298 K and ionic_strength = 0.25 M.

source

eQuilibrator.set_ionic_strength — Method

set_ionic_strength(equilibrator, x)

Set the ionic strength of equilibrator to x.

Example

set_ionic_strength(equilibrator, 100u"mM")

source

eQuilibrator.set_pH — Method

set_pH(equilibrator, x)

Set pH of equilibrator to x.

Example

set_pH(equilibrator, 3.5)

source

eQuilibrator.set_pMg — Method

set_pMg(equilibrator, x)

Set pMg of equilibrator to x.

Example

set_pMg(equilibrator, 1.2)

source

eQuilibrator.set_temperature — Method

set_temperature(equilibrator, x)

Set the temperature of equilibrator to x.

Example

set_temperature(equilibrator, 40u"°C")

source

eQuilibrator.dg_prime — Method

dg_prime(equilibrator, rxn_string; concentrations, balance_warn, skip_unbalanced)

Calculate ΔG' of a reaction described by rxn_string using the settings in equilibrator. Optionally, set the concentrations (abundances) of the species involved in the reaction through concentration. If skip_unbalanced is true then return nothing if the reaction is unbalanced. If balance_warn is false then do not emit a warning when the reaction is unbalanced. Note, concentrations that are smaller than 0.001 mM are capped at 0.001 mM (an eQuilibrator/equilibrator_api) restriction.

Example

equilibrator = Equilibrator()

rxn_string = "bigg.metabolite:atp + bigg.metabolite:h2o = bigg.metabolite:adp + bigg.metabolite:pi"
concens = Dict("bigg.metabolite:atp"=>1u"mM", "bigg.metabolite:adp"=>100u"μM", "bigg.metabolite:pi"=>0.003u"M")
dg_prime(equilibrator, rxn_string; concentrations=concens)

source

eQuilibrator.ln_reversibility_index — Method

ln_reversibility_index(equilibrator, rxn_string; balance_warn, skip_unbalanced)

Calculate the log of the reversibility index of a reaction described by rxn_string using settings in equilibrator. If skip_unbalanced is true then return nothing if the reaction is unbalanced. If balance_warn is false then do not emit a warning when the reaction is unbalanced.

Example

equilibrator = Equilibrator()

rxn_string = "bigg.metabolite:atp + bigg.metabolite:h2o = bigg.metabolite:adp + bigg.metabolite:pi"
ln_reversibility_index(equilibrator, rxn_string)

source

eQuilibrator.physiological_dg_prime — Method

physiological_dg_prime(equilibrator, rxn_string; balance_warn, skip_unbalanced)

Calculate ΔG' at physiological conditions (all concentrations set to 1 mM, 1mbar) of a reaction described by rxn_string using the settings in equilibrator. If skip_unbalanced is true then return nothing if the reaction is unbalanced. If balance_warn is false then do not emit a warning when the reaction is unbalanced.

Example

equilibrator = Equilibrator()

rxn_string = "bigg.metabolite:atp + bigg.metabolite:h2o = bigg.metabolite:adp + bigg.metabolite:pi"
physiological_dg_prime(equilibrator, rxn_string)

source

eQuilibrator.standard_dg_prime — Method

standard_dg_prime(equilibrator, rxn_string; balance_warn, skip_unbalanced)

Calculate ΔG⁰ at standard conditons of a reaction described by rxn_string using the settings in equilibrator. If skip_unbalanced is true then return nothing if the reaction is unbalanced. If balance_warn is false then do not emit a warning when the reaction is unbalanced.

Note, standard conditions means that all concentrations are set at 1 M.

Example

equilibrator = Equilibrator()

rxn_string = "bigg.metabolite:atp + bigg.metabolite:h2o = bigg.metabolite:adp + bigg.metabolite:pi"
standard_dg_prime(equilibrator, rxn_string)

source

eQuilibrator.standard_dg_prime_multi — Method

standard_dg_prime_multi(equilibrator, rxn_strings; balance_warn, skip_unbalanced, uncertainty_representation, minimize_norm)

Calculate ΔG'⁰ for each rxn_string in rxn_strings. The uncertainty_representation can be either fullrank, cov, or sqrt, and is used to represent the uncertainties. Specifically, cov returns a full covariance matrix, precision returna the precision matrix (i.e. the inverse of the covariance matrix), sqrt returns the square root of the covariance, based on the uncertainty vectors, and fullrank returns a full-rank square root of the covariance that is a compressed form of the sqrt result. If minimize_norm is true, an orthogonal projection is used to minimize the Euclidian norm of the result vector. If balance_warn is true, emit a warning if any reaction is unbalanced, if skip_unbalanced is true, return nothing if an unbalanced reaction is found.

Example

equilibrator = Equilibrator()

ntp3 = "gtp + h2o = gdp + pi"
adk3 = "adp + gdp = amp + gtp"

μ, Q = standard_dg_prime_multi(eq, bigg.([ntp3, adk3]); uncertainty_representation="fullrank")

source

eQuilibrator.multi_compartmental_standard_dg_prime — Method

multi_compartmental_standard_dg_prime(equilibrator, rxn_inner, rxn_outer; potential_difference, pH_outer, pMg_outer, ionic_strength_outer, tolerance)

Calculate ΔG'⁰ for a multicompartment reaction. Assume that equilibrator corresponds to the thermodynamic conditions of the inner reaction. The potential_difference across the membrane, as well as the pH_outer, pMg_outer, and ionic_strength_outer can be set. The tolerance sets the allowed imbalance between the rxn_inner and rxn_outer.

Example

equilibrator = Equilibrator()

cyto_rxn = bigg("adp + pi + 2 h = h2o + atp")
peri_rxn = bigg(" = 2 h")

ψ = 0.17u"V"
peri_ionic = 0.2u"M"
peri_pMg = 3.0
peri_pH = 6.5

set_ionic_strength(eq, 250u"mM")
set_pH(eq, 7.4)
set_pMg(eq, 3.0)

dg = multi_compartmental_standard_dg_prime(
    eq,
    cyto_rxn,
    peri_rxn;
    e_potential_difference = ψ,
    pH_outer = peri_pH,
    pMg_outer = peri_pMg,
    ionic_strength_outer = peri_ionic,
    tolerance=2.0,
)

source

eQuilibrator.standard_dg_formation — Method

standard_dg_formation(equilibrator, mets)

Calculate the ΔG'⁰ of formation for all mets, as well as the covariance matrix of the errors.

Example

equilibrator = Equilibrator()

mets = bigg.(["atp", "adp", "amp", "pi", "h2o"])

standard_dgf_prime_mu, standard_dgf_cov = standard_dg_formation(eq, mets)

source

eQuilibrator._lower_bound — Function

_lower_bound(x)
_lower_bound(x, ϵ)

Caps the lower bound of a concentration to ϵ. Return ϵ if x is less than ϵ, otherwise x. This function is not exported.

source

eQuilibrator._parse_reaction_part — Method

_parse_reaction_part(str, prefix)

Helper function for _parse_reaction_string. This function is not exported.

source

eQuilibrator._parse_reaction_string — Method

_parse_reaction_string(str, prefix)

Parse a reaction string and insert the prefix in front of each metabolite. This function is not exported.

source

eQuilibrator._parse_units — Method

_parse_units(x)

Converts units like kilojoule / mole into kJ/mol. This function is not exported.

source

eQuilibrator.bigg — Method

bigg(str)

Return a reaction string that has "bigg.metabolite:" appended in front of each metabolite. Respects stoichiometric coefficients. "*" in front of metabolites do not matter, but spaces do matter. So 13pgm is different from 13 pgm but 13*pgm is the same as 13 pgm. A string literal version also exists: bigg"..."