Package Bio :: Package Pathway :: Class Reaction
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Class Reaction


Abstraction for a biochemical transformation.

This class represents a (potentially reversible) biochemical
transformation of the type:

  a S1 + b S2 + ... --> c P1 + d P2 + ...

where
- a, b, c, d ... are positive numeric stochiometric coefficients,
- S1, S2, ... are substrates
- P1, P2, ... are products

A Reaction should be viewed as the net result of one or more individual
reaction steps, where each step is potentially facilitated by a different
catalyst. Support for 'Reaction algebra' will be added at some point in
the future.

Attributes:

reactants   -- map of involved species to their stochiometric coefficients:
                 reactants[S] = stochiometric constant for S
catalysts   -- list of tuples of catalysts required for this reaction
reversible  -- true iff reaction is reversible
data        -- reference to arbitrary additional data

Invariants:

for all S in reactants.keys(): reactants[S] != 0
for all C in catalysts.keys(): catalysts[C] != 0

Method Summary
  __init__(self, reactants, catalysts, reversible, data)
Initializes a new Reaction object.
  __eq__(self, r)
Returns true iff self is equal to r.
  __hash__(self)
Returns a hashcode for self.
  __ne__(self, r)
Returns true iff self is not equal to r.
  __repr__(self)
Returns a debugging string representation of self.
  __str__(self)
Returns a string representation of self.
  reverse(self)
Returns a new Reaction that is the reverse of self.
  species(self)
Returns a list of all Species involved in self.

Method Details

__init__(self, reactants={}, catalysts=[], reversible=0, data=None)
(Constructor)

Initializes a new Reaction object.

__eq__(self, r)
(Equality operator)

Returns true iff self is equal to r.

__hash__(self)
(Hashing function)

Returns a hashcode for self.

__ne__(self, r)

Returns true iff self is not equal to r.

__repr__(self)
(Representation operator)

Returns a debugging string representation of self.

__str__(self)
(Informal representation operator)

Returns a string representation of self.

reverse(self)

Returns a new Reaction that is the reverse of self.

species(self)

Returns a list of all Species involved in self.

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