This class is used in the Bio.Pathway framework to represent an arbitrary
collection of reactions without explicitly defined links.
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Methods
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__init__
__repr__
__str__
add_reaction
reactions
remove_reaction
species
stochiometry
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__init__
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__init__ ( self, reactions=[] )
Initializes a new System object.
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__repr__
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__repr__ ( self )
Returns a debugging string representation of self.
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__str__
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__str__ ( self )
Returns a string representation of self.
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add_reaction
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add_reaction ( self, reaction )
Adds reaction to self.
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reactions
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reactions ( self )
Returns a list of the reactions in this system.
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remove_reaction
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remove_reaction ( self, reaction )
Removes reaction from self.
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species
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species ( self )
Returns a list of the species in this system.
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stochiometry
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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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