def testHelixThreeRepeats(self):
"""
The find method must find a helix with a repeat count of three.
"""
read = AARead('id', 'FRRRFRRRFRRRF')
landmark = AlphaHelix()
result = list(landmark.find(read))
self.assertEqual([Landmark('AlphaHelix', 'A', 0, 13, 3)], result)
def testConversion(self):
"""
The amino acid sequence must be converted to the right properties
string.
"""
landmark = AlphaHelix()
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', 'AAAFRRRFRRRF')
landmark = AlphaHelix()
result = list(landmark.find(read))
self.assertEqual([Landmark('AlphaHelix', 'A', 3, 9, 2)], result)
def testFindWithOneRepeat(self):
"""
The find method must return an empty generator if there is only one
instance of the OIII pattern
"""
read = AARead('id', 'FRRR')
landmark = AlphaHelix()
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()
result = list(landmark.find(read))
self.assertEqual([], result)
def testTwoHelices(self):
"""
The find method must find more than one helix.
"""
read = AARead('id', 'FRRRFRRRFRFRFRFRFRFRFRFRFRFRFRFFRRRFRRRFRRRF')
landmark = AlphaHelix()
result = list(landmark.find(read))
self.assertEqual([Landmark('AlphaHelix', 'A', 0, 9, 2),
Landmark('AlphaHelix', 'A', 31, 13, 3)],
result)