def testHelixThreeRepeats(self):
"""
The find method must find a helix with a repeat count of three.
"""
read = AARead('id', 'FRRRRFRRRRFRRRRF')
landmark = AlphaHelix_pi()
result = list(landmark.find(read))
self.assertEqual([Landmark('AlphaHelix_pi', 'C', 0, 16, 3)], result)
def testConversion(self):
"""
The amino acid sequence must be converted to the right properties
string.
"""
landmark = AlphaHelix_pi()
result = landmark.convertAAToHydrophobicHydrophilic('ASDGEAHSDTDSCV')
self.assertEqual('OIIIIOOIIOIIOO', result)
def testHelixTwoRepeatsWithNonZeroOffset(self):
"""
The find method must find a helix with a repeat count of two when it
is not at the start of the sequence.
"""
read = AARead('id', 'AAAFRRRRFRRRRF')
landmark = AlphaHelix_pi()
result = list(landmark.find(read))
self.assertEqual([Landmark('AlphaHelix_pi', 'C', 3, 11, 2)], result)
def testFindWithOneRepeat(self):
"""
The find method must return an empty generator if there is only one
instance of the OII pattern
"""
read = AARead('id', 'FRRRR')
landmark = AlphaHelix_pi()
result = list(landmark.find(read))
self.assertEqual([], result)
def testFindWithoutHelix(self):
"""
The find method must return an empty generator when no helix is
present.
"""
read = AARead('id', 'FRFRFRFRFRFRFRFRFRFF')
landmark = AlphaHelix_pi()
result = list(landmark.find(read))
self.assertEqual([], result)
def testTwoHelices(self):
"""
The find method must find more than one helix.
"""
read = AARead('id', 'FRRRRFRRRRFRFRFRFRFRFRFRFRFRFRFFRRRRFRRRRFRRRRF')
landmark = AlphaHelix_pi()
result = list(landmark.find(read))
self.assertEqual([
Landmark('AlphaHelix_pi', 'C', 0, 11, 2),
Landmark('AlphaHelix_pi', 'C', 31, 16, 3)
], result)