psamm.metabolicmodel
– Metabolic model representation¶
Representation of metabolic network models.
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class
psamm.metabolicmodel.
FlipableFluxBounds
(view, reaction)¶ FluxBounds object for a FlipableModelView.
This object is used internally in the FlipableModelView to represent the bounds of flux on a reaction that can be flipped.
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lower
¶ Lower bound
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upper
¶ Upper bound
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class
psamm.metabolicmodel.
FlipableLimitsView
(view)¶ Provides a limits view that flips with the flipable model view.
This object is used internally in FlipableModelView to expose a limits view that flips the bounds of all flipped reactions.
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class
psamm.metabolicmodel.
FlipableModelView
(model, flipped=set([]))¶ Proxy wrapper of model objects allowing a flipped set of reactions.
The proxy will forward all properties normally except that flipped reactions will appear to have stoichiometric values negated in the matrix property, and have bounds in the limits property flipped. This view is needed for some algorithms.
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class
psamm.metabolicmodel.
FlipableStoichiometricMatrixView
(view)¶ Provides a matrix view that flips with the flipable model view.
This object is used internally in FlipableModelView to expose a matrix view that negates the stoichiometric values of flipped reactions.
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class
psamm.metabolicmodel.
FluxBounds
(model, reaction)¶ Represents lower and upper bounds of flux as a mutable object
This object is used internally in the model representation. Changing the state of the object will change the underlying model parameters. Deleting a value will reset that value to the defaults.
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__eq__
(other)¶ Equality test
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__iter__
()¶ Iterator over lower and upper value
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__ne__
(other)¶ Inequality test
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bounds
¶ Bounds as a tuple
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lower
¶ Lower bound
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upper
¶ Upper bound
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class
psamm.metabolicmodel.
LimitsView
(model)¶ Provides a view of the flux bounds defined in the model
This object is used internally in MetabolicModel to expose a dictonary view of the FluxBounds associated with the model reactions.
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class
psamm.metabolicmodel.
MetabolicModel
(database, v_max=1000)¶ Represents a metabolic model containing a set of reactions
The model contains a list of reactions referencing the reactions in the associated database.
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add_all_database_reactions
(compartments)¶ Add all reactions from database that occur in given compartments
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add_all_exchange_reactions
(compartment, allow_duplicates=False)¶ Add all exchange reactions to database and to model
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add_all_transport_reactions
(compartment, allow_duplicates=False)¶ Add all transport reactions to database and to model
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add_reaction
(reaction_id)¶ Add reaction to model
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copy
()¶ Return copy of model
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get_compound_reactions
(compound_id)¶ Iterate over all reaction ids the includes the given compound
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get_reaction_values
(reaction_id)¶ Return stoichiometric values of reaction as a dictionary
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is_exchange
(reaction_id)¶ Whether the given reaction is an exchange reaction.
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is_reversible
(reaction_id)¶ Whether the given reaction is reversible
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classmethod
load_model
(database, reaction_iter=None, medium=None, limits=None, v_max=None)¶ Get model from reaction name iterator
The model will contain all reactions of the iterator.
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remove_reaction
(reaction)¶ Remove reaction from model
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