Bio.Pathway.System

Package Bio :: Package Pathway :: Class System

[show private | hide private]

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

Generated by Epydoc 2.1 on Wed Jan 31 09:58:01 2007

http://epydoc.sf.net