Notes on Working with Rate Objects

Copying

A Rate is not immutable. When we do:

rl = pyna.ReacLibLibrary()
c12ag = rl.get_rate_by_name("c12(a,g)o16")

the rate c12ag is actually a reference to the version stored internally in the Library that ReacLibLibrary creates.

This means if we modify the rate, e.g, as:

c12ag.removed = True

then our library rl is also updated. If we reuse this library, this can have unintended consequences.

As a result, when working with rates that you think may be modified, it is best to work with a copy. The recommended copy is to use the python copy module’s shallow copy:

c12ag_copy = copy.copy(c12ag)

This will invoke a custom __copy__ method in the rate that does a shallow copy for most rate attributes, but explicitly recreates the reactants, products and stoichiometry data.

Tip

When we create a RateCollection or other network, we explicitly copy the rates into the network.