`reconstruction.ecoli.dataclasses.process.equilibrium`

Equilibrium.

class reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium(raw_data, sim_data)[source]

Bases: object

_findColumn(stoichMatrixRow)[source]

_findRow(product, speciesList)[source]

_makeMatrices()[source]: Creates matrix that maps metabolites to the flux through their reactions.

_make_rates()[source]: Creates symbolic representation of the rates for ordinary differential equations and the Jacobian. Used during simulations.

_moleculeRecursiveSearch(product, stoichMatrix, speciesList)[source]

_populateDerivativeAndJacobian()[source]: Compile callable functions for computing the derivative and the Jacobian.

derivatives(t, y)[source]

derivatives_jacobian(t, y)[source]

derivatives_jacobian_jit(t, y)[source]

derivatives_jit(t, y)[source]

fluxes_and_molecules_to_SS(moleculeCounts, cellVolume, nAvogadro, random_state, time_limit=1e+20, max_iter=100, jit=True)[source]

get_fwd_rate(cplxId)[source]

get_metabolite(cplxId)[source]

get_metabolite_coeff(cplxId)[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.

get_rev_rate(cplxId)[source]

get_unbound(cplxId)[source]

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

set_fwd_rate(cplxId, rate)[source]

set_rev_rate(cplxId, rate)[source]

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