Question: how to define new optimization object?

[wyattxuanyang]

Thank you for your great work!

After writing a new Specification class with a "evaluate" method under the folder dnachisel/builtin_specifications(for eg. my_new_optimization_goal.py, similar to EnforceGCContent.py), what else should be done so that my DnaOptimizationProblem can directly use it in a way like
objectives = [my_new_optimization_goal(xxx=, xxx=), CodonOptimize(species='e_coli', location=(500, 1400))]?
Or I just have to put the new class somewhere else?

Thanks,
Wyatt

[Zulko]

Defining evaluate() should be sufficient, although some other methods can additionally be redefined for your new objective if necessary (__str__, localized, initialized_on_problem).

Note that the new optimization objective does NOT need to be added to the library code in builtin_specifications/, it can simply be in the same file or notebook as the rest of your script (see an example here where a new MinimizeNinemersScore is defined just before being used).