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
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Methods
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__eq__
__hash__
__init__
__ne__
__repr__
__str__
reverse
species
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__eq__
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__eq__ ( self, r )
Returns true iff self is equal to r.
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__hash__
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__hash__ ( self )
Returns a hashcode for self.
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__init__
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__init__ (
self,
reactants={},
catalysts=[],
reversible=0,
data=None,
)
Initializes a new Reaction object.
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__ne__
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__ne__ ( self, r )
Returns true iff self is not equal to r.
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__repr__
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__repr__ ( self )
Returns a debugging string representation of self.
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__str__
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__str__ ( self )
Returns a string representation of self.
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Exceptions
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AttributeError, "Invalid 0 coefficient in Reaction.reactants"
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reverse
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reverse ( self )
Returns a new Reaction that is the reverse of self.
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species
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species ( self )
Returns a list of all Species involved in self.
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