psamm.fastcore
– Fastcore (approximate consistent subset)¶
Fastcore module implementing the fastcore algorithm
This is an implementation of the algorithms described in [Vlassis14].
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exception
psamm.fastcore.
FastcoreError
¶ Indicates an error while running Fastcore
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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.
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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.
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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.
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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.