psamm.fastcore – Fastcore (approximate consistent subset)

Fastcore module implementing the fastcore algorithm

This is an implementation of the algorithms described in [Vlassis14].

exception psamm.fastcore.FastcoreError

Indicates an error while running Fastcore

psamm.fastcore.fastcc(model, epsilon, solver)

Check consistency of model reactions

Yields all reactions in the model that are not part of the consistent subset.

psamm.fastcore.fastcc_consistent_subset(model, epsilon, solver)

Return consistent subset of model

The largest consistent subset is returned as a set of reaction names.

psamm.fastcore.fastcc_is_consistent(model, epsilon, solver)

Quickly check whether model is consistent

Returns true if the model is consistent. If it is only necessary to know whether a model is consistent, this function is faster as it will return the result as soon as it finds a single inconsistent reaction.

psamm.fastcore.fastcore(model, core, epsilon, solver, scaling=100000.0, weights={})

Find a flux consistent subnetwork containing the core subset

The result will contain the core subset and as few of the additional reactions as possible.