standard_dg_prime() function doesn't work with PhasedCompounds
When I try to calculate the standard_dg_prime from a ThermodynamicModel object, I get the following error:
AttributeError: 'PhasedCompound' object has no attribute 'transform'
It looks like the standard_dg_prime() function is expecting PhasedReaction objects that contain Compound objects, but is instead getting a PhasedReaction object that contains PhasedCompound objects.
Here's some minimal code to reproduce:
from equilibrator_api import ComponentContribution, Q_
from equilibrator_pathway import ThermodynamicModel
cc = ComponentContribution()
pp = ThermodynamicModel.from_sbtab("examples_pyr_etoh_mdf.tsv", comp_contrib=cc)
r1 = pp.net_reaction
cc.physiological_dg_prime(r1)
If I manually parse the net formula, things work fine
r2 = cc.parse_reaction_formula("bigg.metabolite:for + bigg.metabolite:h + bigg.metabolite:pyr = 2 bigg.metabolite:co2 + bigg.metabolite:etoh")
cc.physiological_dg_prime(r2)
I'm using equilibrator-api v 0.4.7, equilibrator-cache v 0.4.3, and equilibrator-pathway v 0.4.7