reconstruction.ecoli.dataclasses.process.equilibrium
Equilibrium.
- class reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium(raw_data, sim_data)[source]
Bases:
object
- _make_rates()[source]
Creates symbolic representation of the rates for ordinary differential equations and the Jacobian. Used during simulations.
- _populateDerivativeAndJacobian()[source]
Compile callable functions for computing the derivative and the Jacobian.
- fluxes_and_molecules_to_SS(moleculeCounts, cellVolume, nAvogadro, random_state, time_limit=1e+20, max_iter=100, jit=True)[source]
- get_monomers(cplxId)[source]
Returns subunits for a complex (or any ID passed). If the ID passed is already a monomer returns the monomer ID again with a stoichiometric coefficient of one.
- mass_balance()[source]
Sum along the columns of the massBalance matrix to check for reaction mass balance
- mass_matrix()[source]
Builds stoichiometry mass matrix Rows: molecules Columns: reactions Values: molecular mass
- stoich_matrix()[source]
Builds stoichiometry matrix Rows: molecules Columns: reactions Values: reaction stoichiometry
- stoich_matrix_monomers()[source]
Builds a stoichiometric matrix where each column is a reaction that forms a complex directly from its constituent monomers. Since some reactions from the raw data are complexation reactions of complexes, this is different from the stoichiometric matrix generated by stoichMatrix().
- exception reconstruction.ecoli.dataclasses.process.equilibrium.EquilibriumError[source]
Bases:
Exception
- exception reconstruction.ecoli.dataclasses.process.equilibrium.MoleculeNotFoundError[source]
Bases:
EquilibriumError