def test_find_secstruc_elements_bulge(self):
result = Secstruc(BULGE_SS).find_secstruc_elements()
self.assertTrue(Secstruc('(....)',[5,6,7,8,9,10]) in result)
self.assertTrue(Secstruc('(().)',[3,4,11,12,13]) in result)
self.assertTrue(Secstruc('(())',[4,5,10,11]) in result)
self.assertTrue(Secstruc('(((())))',[0,1,2,3,13,14,15,16]) in result)
self.assertEqual(len(result), 4)
def test_find_junctions(self):
"""Should return all junctions from a secstruc."""
junctions = Secstruc('(()()())').find_junctions()
self.assertEqual(junctions[0], Secstruc('(()()())'))
# helices should be no junctions
junctions = Secstruc('((()))').find_junctions()
self.assertEqual(len(junctions), 0)
def test_find_bulges(self):
"""Should return all bulges from a secstruc."""
bulges = Secstruc(BULGE_SS).find_bulges()
self.assertEqual(len(bulges),1)
self.assertEqual(bulges[0], Secstruc('(().)',[3,4,11,12,13]))
# also check bulge in other direction
bulges = Secstruc("((.((..))))").find_bulges()
self.assertEqual(bulges[0], Secstruc('(.())',[1,2,3,8,9]))
def setUp(self):
self.hairpin = Secstruc(HAIRPIN_SS)
self.bulge = Secstruc(BULGE_SS)
self.internal_loop = Secstruc(INTERNAL_LOOP_SS)
self.junction = Secstruc(JUNCTION_SS)
self.helix = Secstruc("((()))",[0,1,2,6,7,8])
self.helix_shifted = Secstruc("((()))",[2,3,4,8,9,10])
self.helix_a = Secstruc("(((",[0,1,2])
self.helix_b = Secstruc(")))",[6,7,8])
def test_find_secstruc_elements_junction(self):
result = Secstruc(JUNCTION_SS).find_secstruc_elements()
self.assertTrue(Secstruc('..(',[0,1,2]) in result)
self.assertTrue(Secstruc('((()))',[2,3,4,27,28,29]) in result)
self.assertTrue\
(Secstruc('(..().())',[4,5,6,7,17,18,19,26,27]) in result)
self.assertTrue(Secstruc('(((())))',[7,8,9,10,14,15,16,17]) in result)
self.assertTrue(Secstruc('(...)',[10,11,12,13,14]) in result)
self.assertTrue(Secstruc('(())',[19,20,25,26]) in result)
self.assertTrue(Secstruc('(....)',[20,21,22,23,24,25]) in result)
self.assertEqual(len(result), 7)
def test_find_helices(self):
"""Should return all helices from a secstruc."""
# simple helix
helices = Secstruc("...(())..").find_helices()
self.assertEqual(len(helices),1)
self.assertEqual(helices[0], Secstruc('(())', [3,4,5,6]))
# multiple helices
helices = Secstruc(".(())...((..)).((()))()..").find_helices()
self.assertEqual(len(helices),4)
# full helix in one.
helices = Secstruc("((()))").find_helices()
self.assertEqual(helices[0], Secstruc('((()))',[0,1,2,3,4,5]))
# two helices with bulge in between
helices = Secstruc("((((((..))).)))").find_helices()
self.assertEqual(len(helices),2)
self.assertEqual(helices[0], Secstruc('((()))',[0,1,2,12,13,14]))
self.assertEqual(helices[1], Secstruc('((()))',[3,4,5,8,9,10]))
def test_find_loops(self):
"""Should return all loops from a secstruc."""
loops = Secstruc("(((..))).").find_loops()
self.assertEqual(loops[0], Secstruc('(..)',[2,3,4,5]))
def test_find_overhang3(self):
"""Should part the object into an overhang secstruc."""
# 3'-overhangs
overhang = Secstruc("(((..)))....").find_overhang3()
self.assertEqual(overhang, Secstruc(')....',[7,8,9,10,11]))
def test_find_overhang5(self):
"""Should part the object into an overhang secstruc."""
# 5'-overhangs
overhang = Secstruc("..((()))").find_overhang5()
self.assertEqual(overhang, Secstruc('..(',[0,1,2]))
def test_get_type(self):
"""Should recognize substructures."""
self.assertEqual(Secstruc('()').get_type(),None)
self.assertEqual(Secstruc('((()))').get_type(),'helix')
self.assertEqual(Secstruc('((())))').get_type(),None)
self.assertEqual(Secstruc('(())').get_type(),'helix')
self.assertEqual(Secstruc('...(').get_type(),"5'-overhang")
self.assertEqual(Secstruc(').').get_type(),"3'-overhang")
self.assertEqual(Secstruc('(....)').get_type(),'loop')
self.assertEqual(Secstruc('(().)').get_type(),'bulge')
self.assertEqual(Secstruc('(.())').get_type(),'bulge')
self.assertEqual(Secstruc('(..())').get_type(),'bulge')
self.assertEqual(Secstruc('(..().())').get_type(),'junction')
self.assertEqual(Secstruc('(()()())').get_type(),'junction')
def test_get_bp_array(self):
s = Secstruc(".(())...((..)).((()))()..")
self.assertEqual(s.get_bp_array(), [-1, 4, 3, 2, 1, -1, -1, -1, \
13, 12, -1, -1, 9, 8, -1, 20, 19, 18, 17, 16, 15, 22, 21, -1, -1])
def test_getitem(self):
self.assertEqual(self.helix[2], Secstruc("(",[2]))
self.assertEqual(self.helix[3], Secstruc(")",[6]))
def test_slice(self):
a = self.helix[:3]
self.assertEqual(a, self.helix_a)
b = self.helix[3:]
self.assertEqual(b, self.helix_b)
self.assertEqual(self.helix[2:4], Secstruc("()",[2,6]))
def test_eq(self):
self.assertEqual(self.helix,Secstruc("((()))",[0,1,2,6,7,8]))
self.assertNotEqual(self.helix, self.helix_a)
self.assertNotEqual(self.helix_a, self.helix_b)
self.assertNotEqual(self.helix, self.helix_shifted)
self.assertEqual(self.hairpin, "((((...))))")
def test_find_secstruc_elements(self):
"""Should divide a sec struct into substructures and their indices."""
result = Secstruc(HAIRPIN_SS).find_secstruc_elements()
self.assertTrue(Secstruc('(...)',[3,4,5,6,7]) in result)
self.assertTrue(Secstruc('(((())))',[0,1,2,3,7,8,9,10]) in result)
self.assertEqual(len(result), 2)
def test_find_internal_loop(self):
"""Internal loops should be recognized as bulges."""
loops = Secstruc(INTERNAL_LOOP_SS).find_bulges()
self.assertEqual(len(loops),1)
self.assertEqual(loops[0], Secstruc('(....()..)',\
[2,3,4, 5, 6, 7, 15, 16, 17, 18]))