Package Bio :: Package Pathway :: Class System
[hide private]
[frames] | no frames]

Class System

source code

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
Method Details [hide private]

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