from nupack import *

my_model = Model(material='dna', celsius=37,sodium=0.1, magnesium=0.02)

c = Domain('N8',        name='c')
cc = Domain('N3',        name='cc')
cc2 = Domain('N3',        name='cc2')
d = Domain('N8',        name='d')
e = Domain('N7R1',        name='e')
f = Domain('N10',        name='f')
g = Domain('N8',        name='g')
k = Domain('N8',        name='k')
h = Domain('N15R1',        name='h')
hh = Domain('N6',        name='hh')
E = Domain('GGCTAGCTACAACGA',        name='E')

E1 = TargetStrand([h, E, ~e, ~c], name='Strand E1')
F1 = TargetStrand([~f, ~d, ~g, ~k, f, c, e, hh], name='Strand F1')

E1F1 = TargetComplex([E1, F1], '.10(6.15(16+(10.24)32', name='E1F1')

t1 = TargetTube(on_targets={E1F1: 1e-8}, name='t1',
    off_targets=SetSpec(max_size=4))

pattern = Pattern(['A4', 'C4', 'G4', 'U4', 'T4'])
my_tubes = [t1,t2]
my_design = tube_design(tubes=my_tubes,
    hard_constraints=[pattern],model=my_model)
my_result = my_design.run(trials=1)
print(my_result)