Thermoqp¶

thermoFlux2QNty(model, solution, param)[source]¶

Given a steady state thermodynamically feasible flux vector, v, such that

S*v = b

l <= v <= u

Compute q and g = N’*y such that

N*diag(q)*g = b - B*w

where the stoichiometric matrix and flux vector are split into internal and external components: S = [N B] and v = [z; w],

thermoQP(model, q, param)[source]¶

Compute an approximately thermodynamically feasible flux by minimising the Euclidean norm, weighted by the conductances provided in q.

INPUT

model – (the following fields are required - others can be supplied)
- S - m x 1 Stoichiometric matrix
- c - n x 1 Linear objective coefficients
- lb - n x 1 Lower bounds
- ub - n x 1 Upper bounds
q – n x 1 vector of reaction conductances

OPTIONAL INPUTS

model –
- dxdt - m x 1 change in concentration with time
- csense - m x 1 character array with entries in {L,E,G} (The code is backward compatible with an m + k x 1 csense vector, where k is the number of coupling constraints)
- C - k x n Left hand side of C*v <= d
- d - k x n Right hand side of C*v <= d
- dsense - k x 1 character array with entries in {L,E,G}
osenseStr – Maximize (‘max’)/minimize (‘min’) (opt, default = ‘max’)

OUTPUT

sol – sol object: