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Package Bio :: Package Pathway :: Class System
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Class System

source code

object --+
         |
        System

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:

None
Instance Methods [hide private]
 
__init__(self, reactions=[])
Initializes a new System object.		 source code
 
__repr__(self)
Returns a debugging string representation of self.		 source code
 
__str__(self)
Returns a string representation of self.		 source code
 
add_reaction(self, reaction)
Adds reaction to self.		 source code
 
remove_reaction(self, reaction)
Removes reaction from self.		 source code
 
reactions(self)
Returns a list of the reactions in this system.		 source code
 
species(self)
Returns a list of the species in this system.		 source code
 
stochiometry(self)
Computes the stoichiometry matrix for self.		 source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, reactions=[])
(Constructor)

source code  
Initializes a new System object.
Overrides: object.__init__

__repr__(self)
(Representation operator)

source code  
Returns a debugging string representation of self.
Overrides: object.__repr__

__str__(self)
(Informal representation operator)

source code  
Returns a string representation of self.
Overrides: object.__str__

reactions(self)

source code  
Returns a list of the reactions in this system.

Note the order is arbitrary!

stochiometry(self)

source code  
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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