Class Reaction

source code

object --+
         |
        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: reactants[S] != 0
for all C in catalysts: catalysts[C] != 0