Example usage

The following examples follow closely the example usage documented in equilibrator_api. Try running these examples!

Basic ΔG' calculations

Load eQuilibrator.jl and Unitful. Then initialize the thermodynamic equilibrator as shown below.

using eQuilibrator
using Unitful

temp = 30u"°C"
i_strength = 150.0u"mM"
ph = 7.9
pmg = 2.0

equilibrator = eQuilibrator.Equilibrator(pH=ph, pMg=pmg, temperature=temp, ionic_strength=i_strength)

Take care of units

Units for temperature and ionic strength are required (pH and pMg are unitless floats). However, any suitable unit may be used, they are internally converted into Kelvin and molar respectively.

Temperature

Please see the documentation of eQuilibrator or equilibrator-api about changing the temperature.

It is possible to change the state of the equilibrator after initialization.

set_temperature(equilibrator, 298.15u"K")
set_ionic_strength(equilibrator, 0.25u"M")
set_pH(equilibrator, 7.4)
set_pMg(equilibrator, 3.0)

An eQuilibrator.jl Equilibrator has pretty printing:

julia> eq
Interface to equilibrator_api v0.4.5.1
Temperature:    298.15 K
Ionic strength: 0.25 M
pH:             7.5
pMg:            3.0

It is necessary to supply a reaction string.

rxn_string = "bigg.metabolite:atp + bigg.metabolite:h2o = bigg.metabolite:adp + bigg.metabolite:pi"

After specifying the reaction string, it is a simple matter of calling the appropriate function to get the ΔG values.

physiological_dg_prime(equilibrator, rxn_string)
# -46.26 ± 0.3 kJ mol^-1

standard_dg_prime(equilibrator, rxn_string)
# -29.14 ± 0.3 kJ mol^-1

dg_prime(equilibrator, rxn_string) # equilibrator_api default abundances/concentrations
# -29.14 ± 0.3 kJ mol^-1

concens = Dict("bigg.metabolite:atp"=>1u"mM", "bigg.metabolite:adp"=>100u"μM", "bigg.metabolite:pi"=>0.005u"M")
dg_prime(equilibrator, rxn_string; concentrations=concens) # user specified concentrations
# -47.98 ± 0.3 kJ mol^-1

ln_reversibility_index(equilibrator, rxn_string)
# -12.447 ± 0.082

Errors are shown using `Measurements.jl`

eQuilibrator supplies estimates with uncertainties, these are reflected by the use of a ± b with b being the uncertainty, assumed to be one standard deviation here. The nominal value of a Gibbs energy estimate may be found by using Measurements.value(...).

Units are shown using `Unitful.jl`

Units are associated with each Gibbs energy estimate. To remove the units, use Unitful.ustrip(...).

Reaction parsing

It is possible to mix and match metabolite identifiers, exactly like in equilibrator_api, with the associated warnings. In short, the reaction string is directly passed to equilibrator_api, so whatever strings works for it, will also work here.

equilibrator = eQuilibrator.Equilibrator()
atpase_rxn_string_2 = "kegg:C00002 + CHEBI:15377 = metanetx.chemical:MNXM7 + bigg.metabolite:pi"
dg_prime(equilibrator, atpase_rxn_string_2)
# -27.37 ± 0.3 kJ mol^-1

Convenience functions for reaction string processing are also made available. These functions insert the appropriate identifier in front of each metabolite while respecting the associated stoichiometric coefficient. Note, these functions insert the exact same prefix before each metabolite.

bigg("atp + h2o = adp + pi")
# "bigg.metabolite:atp + bigg.metabolite:h2o = bigg.metabolite:adp + 2 bigg.metabolite:pi"

bigg"atp + h2o = adp + pi"
# "bigg.metabolite:atp + bigg.metabolite:h2o = bigg.metabolite:adp + 2 bigg.metabolite:pi"

kegg("C00002 + C00001 = C00008 + C00009")
# "kegg:C00002 + kegg:C00001 = kegg:C00008 + kegg:C00009"

kegg"C00002 + C00001 = C00008 + C00009"
# "kegg:C00002 + kegg:C00001 = kegg:C00008 + kegg:C00009"

metanetx("MNXM3 + MNXM2 = MNXM7 + MNXM9")
# "metanetx.chemical:MNXM3 + metanetx.chemical:MNXM2 = metanetx.chemical:MNXM7 + metanetx.chemical:MNXM9"

metanetx"MNXM3 + MNXM2 = MNXM7 + MNXM9"
# "metanetx.chemical:MNXM3 + metanetx.chemical:MNXM2 = metanetx.chemical:MNXM7 + metanetx.chemical:MNXM9"

chebi("30616 + 33813 = 456216 + 43474")
# "CHEBI:30616 + CHEBI:33813 = CHEBI:456216 + CHEBI:43474"

chebi"30616 + 33813 = 456216 + 43474"
# "CHEBI:30616 + CHEBI:33813 = CHEBI:456216 + CHEBI:43474"

To use this functionality:

equilibrator = eQuilibrator.Equilibrator()
r_str = bigg"atp + h2o = adp + pi"
dg_prime(equilibrator, r_str)
# -27.37 ± 0.3 kJ mol^-1

Note, these convenience functions may also be used on single metabolites to simplify the specification of metabolite concentrations for dg_prime:

equilibrator = eQuilibrator.Equilibrator()
r_string = bigg"atp + h2o = adp + pi"
concens = [bigg"atp"=>1u"mM", bigg"adp"=>100u"μM", bigg"pi"=>0.005u"M"]
dg_prime(equilibrator, r_string; concentrations=concens) # user specified concentrations
# -46.2 ± 0.3 kJ mol^-1

Advanced functionality

This API is relatively complete, see the test directory for all the implemented functionality. In short, multi-compartment and multi-reaction functionality is implemented, as well as limited Gibbs energy of formation support.