def test_DSD_ComplexDomains(self):
foo = bc.DSD_Complex(sequence=
[self.d1, self.d2, self.d3, '+', self.d1, '+', self.d1c, self.d3c, self.d1c, self.d2],
structure=list('..(+(+))..'))
self.assertEqual(foo.sequence,
[self.d1, self.d2, self.d3, '+', self.d1, '+', self.d1c, self.d3c, self.d1c, self.d2])
self.assertEqual(foo.lol_sequence,
[[self.d1, self.d2, self.d3], [self.d1], [self.d1c, self.d3c, self.d1c, self.d2]])
bc.clear_memory()
bar = bc.DSD_Complex(sequence=
[self.d1c, self.d3c, self.d1c, self.d2, '+', self.d1, self.d2, self.d3, '+', self.d1],
structure=list('((..+..)+)'))
self.assertEqual(foo, bar)
self.assertTrue(foo == bar)
def test_initialize(self):
with self.assertRaises(bc.DSDObjectsError):
x = bc.DSD_Reaction(['A','B','C'],['D','A','E'], rtype = 'branch-3way')
A = bc.DSD_Complex(list('NNNNNNN'), list('((...))'), name='A')
B = bc.DSD_Complex(list('NNNNNNN'), list('.(...).'), name='B')
x = bc.DSD_Reaction([A, B],[B, B], rtype = 'branch-3way')
with self.assertRaises(bc.DSDDuplicationError):
y = bc.DSD_Reaction([A, B],[B, B], rtype = 'branch-3way')
bc.clear_memory()
y = bc.DSD_Reaction([A, B],[B, B], rtype = 'branch-3way', rate=.5)
z = bc.DSD_Reaction([A],[B], rtype='bind11')
self.assertEqual('A + B -> B + B', str(x))
A.name = 'Z'
self.assertEqual('Z + B -> B + B', str(x))
self.assertEqual('Z + B -> B + B', str(y))
self.assertEqual(x, y)
with self.assertRaises(bc.DSDDuplicationError):
y = bc.DSD_Reaction([A, B],[B, B], rtype = 'branch-3way')
self.assertEqual(x, y)
self.assertTrue(x != z)
self.assertEqual(y.rate.constant, .5)
self.assertEqual(y.const, .5)
self.assertEqual(y.rateunits, '/M/s')
x = y.rateformat(['M','s'])
self.assertEqual(x.constant, 0.5)
x = y.rateformat(['mM','s'])
self.assertEqual(x.constant, 0.0005)
x = y.rateformat(['uM','s'])
self.assertEqual(x.constant, 0.0000005)
x = y.rateformat(['nM','s'])
self.assertEqual(x.constant, 0.0000000005)
x = y.rateformat(['pM','s'])
self.assertEqual(x.constant, 0.0000000000005)
y.rate = y.rateformat(['mM','s'])
self.assertEqual(y.rate.constant, 0.0005)
def tearDown(self):
bc.clear_memory()