def main():
# o1 = create_test0() # just a fully hybridized strand.
# o1 = create_test0B() # just a fully hybridized strand.
# o1 = create_test0C() # just a fully hybridized strand.
# o1 = create_test1() # testing open-loop
# o1 = create_test1B() # testing open-loop with the initialiation penalty
# o1 = create_test2() # a very simple test being .(.+.).
o1 = create_test2B() # a very simple test being .(.+.).
# o1.bimolecular_scaling = 777.0
o1.DNA23Metropolis()
# o1 = create_test3() # this is the bi-molecular test
# o1 = create_test4() # this is the lightbulb
# o1 = create_test5() # testing multi-loop code
# o1 = create_test6() # interior loop.
# o1 = create_test6B() # small interior loop.
# o1 = create_test7() # Bulge loop.
# o1 = create_test8() # Hairpin loop.
# o1 = create_test9() # Small open-loop code
# o1 = create_test10() # half open duplex
# o1 = create_test11() # Oscillator gate
# o1 = create_test12() # displacement situation.
# o1 = create_test13() # this is a test for dissociation
# setArrheniusConstantsNM1(o1)
# o1.DNA23Metropolis()
s = SimSystem(o1)
# s.start()
s.initialInfo()
def main():
# o1 = create_test0() # just a fully hybridized strand.
# o1 = create_test0B() # just a fully hybridized strand.
# o1 = create_test0C() # just a fully hybridized strand.
# o1 = create_test1() # testing open-loop
# o1 = create_test1B() # testing open-loop with the initialiation penalty
# o1 = create_test2() # a very simple test
# o1 = create_test3() # this is the bi-molecular test
# o1 = create_test4() # this is the lightbulb
# o1 = create_test5() # testing multi-loop code
# o1 = create_test6() # interior loop.
# o1 = create_test6B() # small interior loop.
# o1 = create_test7() # Bulge loop.
# o1 = create_test8() # Hairpin loop.
# o1 = create_test9() # Small open-loop code
# o1 = create_test10() # half open duplex
o1 = create_test11() # Oscillator gate
# setArrheniusConstantsNM1(o1)
s = SimSystem(o1)
# s.start()
s.initialInfo()
def main2():
o1 = create_setup_interal(toehold_t, toehold_dd, domain_R, 25)
s = SimSystem(o1)
s.initialInfo()
print "Testing loop internals"
def initialInfo(self):
myOptions = self.factory.new(777)
simSys = SimSystem(myOptions)
simSys.initialInfo()
def main():
o1 = create_test10() # half open duplex
s = SimSystem(o1)
s.initialInfo()
