thtools.utils.ModelNu3¶
- class thtools.utils.ModelNu3(wobble=None, kelvin=None, celsius=37, sodium=1.0, magnesium=0.0)¶
Class to emulate the behaviour of NUPACK v3.
A thermodynamic model subclassing
nupack.Model
which mimics the NUPACK website .- Parameters
- wobblebool, optional
- kelvinfloat, optional
- celsiusfloat, optional, default = 37
- sodiumfloat, default = 1.0
- magnesiumfloat, default = 0.0
Examples
>>> import thtools as tt >>> ths = "UUAGCCGCUGUCACACGCACAGGGAUUUACAAAAAGAGGAGAGUAAAAUGCUGUGCGUGCACCAUAAAACGAACAUAGAC" >>> rbs = "AGAGGAGA" >>> triggers = ["CUGUGCGUGUGACAGCGGCUGA", "CUAUACAAUCUACUGUCUUUCC", "UGUACAGCCUCCUAGCUUUCC"] >>> model = tt.ModelNu3(celsius=21.0) >>> my_test = tt.autoconfig(ths, rbs, triggers, model=model) >>> my_result = my_test.run(max_size=3, n_samples=100) >>> my_result.specificity # gives as decimal, not percentage 1.0