Package Bio :: Package Pathway :: Class System
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Class 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
Method Summary
  __init__(self, reactions)
Initializes a new System object.
  __repr__(self)
Returns a debugging string representation of self.
  __str__(self)
Returns a string representation of self.
  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.

Method Details

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

Initializes a new System object.

__repr__(self)
(Representation operator)

Returns a debugging string representation of self.

__str__(self)
(Informal representation operator)

Returns a string representation of self.

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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