reconstruction.ecoli.dataclasses.process.complexation

SimulationData for the Complexation process

class reconstruction.ecoli.dataclasses.process.complexation.Complexation(raw_data, sim_data)

Bases: object

_buildStoichMatrixMonomers()

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().

_findColumn(stoichMatrixRow)

_findRow(product, speciesList)

_moleculeRecursiveSearch(product, stoichMatrix, speciesList)

get_monomers(cplxId)

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_matrix()

Builds a matrix with the same shape as the stoichiometric matrix, but with molecular masses as elements instead of stoichiometric constants

stoich_matrix()

Builds a stoichiometric matrix based on each given complexation reaction. One reaction corresponds to one column in the stoichiometric matrix.

stoich_matrix_monomers()

Returns the dense stoichiometric matrix for monomers from each complex

exception reconstruction.ecoli.dataclasses.process.complexation.ComplexationError

Bases: Exception

exception reconstruction.ecoli.dataclasses.process.complexation.MoleculeNotFoundError

Bases: ComplexationError