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Package Bio :: Package Pathway :: Class System |
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Abstraction for a collection of reactions.
This class is used in the Bio.Pathway framework to represent an arbitrary collection of reactions without explicitly defined links.
Attributes:
NoneMethod Summary | |
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Initializes a new System object. | |
Returns a debugging string representation of self. | |
Returns a string representation of self. | |
Adds reaction to self. | |
Returns a list of the reactions in this system. | |
Removes reaction from self. | |
Returns a list of the species in this system. | |
Computes the stoichiometry matrix for self. |
Method Details |
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__init__(self,
reactions=[])
Initializes a new System object.
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__repr__(self)
Returns a debugging string representation of self.
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__str__(self)
Returns a string representation of self.
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add_reaction(self, reaction)Adds reaction to self. |
reactions(self)Returns a list of the reactions in this system. |
remove_reaction(self, reaction)Removes reaction from self. |
species(self)Returns a list of the species in this system. |
stochiometry(self)Computes the stoichiometry matrix for self. Returns (species, reactions, stoch) where species = ordered list of species in this system reactions = ordered list of reactions in this system stoch = 2D array where stoch[i][j] is coef of the jth species in the ith reaction, as defined by species and reactions above |
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