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