def GetTransfromedReactionEnergies(self,
S,
cids,
pH=None,
I=None,
pMg=None,
T=None,
conc=1):
dG0_r = PsuedoisomerTableThermodynamics.GetTransfromedReactionEnergies(
self, S, cids, pH, I, pMg, T)
if conc != 1:
pH, I, pMg, T = self.GetConditions(pH, I, pMg, T)
dG0_r += AddConcentrationsToReactionEnergies(S, cids, T, conc)
# find the mapping between the list of all CIDs and the list that the
# new S is using
all_cids = sorted(self.kegg.get_all_cids())
inds = [all_cids.index(cid) for cid in cids]
# test to see if any of the reactions in S violate any conservation laws
violations = abs(self.P_L_tot[:, inds] * S).sum(0) > self.epsilon
dG0_r[violations] = np.nan
return dG0_r
