psamm.massconsistency – Mass consistency check

Mass consistency analysis of metabolic databases

A stoichiometric matrix, S, is said to be mass-consistent if S^Tm = 0 has a positive solution (m_i > 0). This corresponds to assigning a positive mass to each compound in the stoichiometric matrix and having each reaction preserve mass. Exchange reactions will have to be excluded from this check, as they are not able to preserve mass (by definition). In addition some databases may contain pseudo-compounds (e.g. “photon”) that also has to be excluded.

exception psamm.massconsistency.MassConsistencyError

Indicates an error while checking for mass consistency

psamm.massconsistency.check_compound_consistency(database, solver, exchange=set([]), zeromass=set([]))

Yield each compound in the database with assigned mass

Each compound will be assigned a mass and the number of compounds having a positive mass will be approximately maximized.

This is an implementation of the solution originally proposed by [Gevorgyan08] but using the new method proposed by [Thiele14] to avoid MILP constraints. This is similar to the way Fastcore avoids MILP contraints.

psamm.massconsistency.check_reaction_consistency(database, solver, exchange=set([]), checked=set([]), zeromass=set([]), weights={})

Check inconsistent reactions by minimizing mass residuals

Return a reaction iterable, and compound iterable. The reaction iterable yields reaction ids and mass residuals. The compound iterable yields compound ids and mass assignments.

Each compound is assigned a mass of at least one, and the masses are balanced using the stoichiometric matrix. In addition, each reaction has a residual mass that is included in the mass balance equations. The L1-norm of the residuals is minimized. Reactions in the checked set are assumed to have been manually checked and therefore have the residual fixed at zero.

psamm.massconsistency.is_consistent(database, solver, exchange=set([]), zeromass=set([]))

Try to assign a positive mass to each compound

Return True if successful. The masses are simply constrained by m_i > 1 and finding a solution under these conditions proves that the database is mass consistent.