def testEmptyRead(self):
"""
An empty read must not return any landmarks.
"""
read = SSAARead('id', '', '')
landmark = PDB_ExtendedStrand()
result = landmark.find(read)
self.assertEqual([], list(result))
def testNoLandmarks(self):
"""
A read that has no landmarks must result in an empty list.
"""
read = SSAARead('id', 'RFRFRFRFR', 'HHHHHHHHH')
landmark = PDB_ExtendedStrand()
result = landmark.find(read)
self.assertEqual([], list(result))
def testNoLandmarks(self):
"""
A read that has no landmarks must result in an empty list.
"""
read = SSAARead('id', 'RFRFRFRFR', 'GGGGGGGGG')
landmark = PDB_AlphaHelix()
result = landmark.find(read)
self.assertEqual([], list(result))
def testEmptyRead(self):
"""
An empty read must not return any landmarks.
"""
read = SSAARead('id', '', '')
landmark = PDB_AlphaHelix_combined()
result = landmark.find(read)
self.assertEqual([], list(result))
def testOneLandmarkAtEnd(self):
"""
If the structure sequence has the landmark at its end, the right
landmark must be returned.
"""
read = SSAARead('id', 'RFRFRFRFR', 'HHHHHHEEE')
landmark = PDB_ExtendedStrand()
result = landmark.find(read)
self.assertEqual([Landmark('PDB ExtendedStrand', 'PDB-ES', 6, 3)],
list(result))
def testOneLandmarkAtEnd(self):
"""
If the structure sequence has the landmark at its end, the right
landmark must be returned.
"""
read = SSAARead('id', 'RFRFRFRFR', 'GGGGGGHHH')
landmark = PDB_AlphaHelix()
result = landmark.find(read)
self.assertEqual([Landmark('PDB AlphaHelix', 'PDB-A', 6, 3)],
list(result))
def testOneLandmarkInMiddle(self):
"""
If the structure sequence has the landmark in the middle, the right
landmark must be returned.
"""
read = SSAARead('id', 'RFRFRFRFR', 'GGHHHGGGG')
landmark = PDB_AlphaHelix()
result = landmark.find(read)
self.assertEqual([Landmark('PDB AlphaHelix', 'PDB-A', 2, 3)],
list(result))
def testOneLandmarkAtStart(self):
"""
If the structure sequence has the landmark at its beginning, the right
landmark must be returned.
"""
read = SSAARead('id', 'RFRFRFRFR', 'IIIHHHHHH')
landmark = PDB_AlphaHelix_pi()
result = landmark.find(read)
self.assertEqual([Landmark('PDB AlphaHelix_pi', 'PDB-Api', 0, 3)],
list(result))
def testAlphaHelixMixtureMustBeFound(self):
"""
If the stucture sequence contains all alpha helix types ('H', 'G',
'I'), the right landmark must be returned.
"""
read = SSAARead('id', 'RFRFRFRFR', 'HGISSSSSS')
landmark = PDB_AlphaHelix_combined()
result = landmark.find(read)
self.assertEqual([Landmark('PDB AlphaHelix_combined', 'PDB-AC', 0, 3)],
list(result))
def testTwoLandmarks(self):
"""
The right landmarks must be returned when a structure sequence with
two landmarks is given.
"""
read = SSAARead(
'id', 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA',
'-EEEEEEEEEEEEEEEEEEEEEEEEEET-TT-TTSS---TTT-TTEEEE-SS---')
landmark = PDB_ExtendedStrand()
result = landmark.find(read)
self.assertEqual([
Landmark('PDB ExtendedStrand', 'PDB-ES', 1, 26),
Landmark('PDB ExtendedStrand', 'PDB-ES', 45, 4)
], list(result))
def testTwoLandmarks(self):
"""
The right landmarks must be returned when a structure sequence with
two landmarks is given.
"""
read = SSAARead(
'id',
'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA',
'-HHHHHHHHHHHHHHHHHHHHHHHHHHT-TT-TTSS---TTT-TTHHHH-SS---')
landmark = PDB_AlphaHelix()
result = landmark.find(read)
self.assertEqual([Landmark('PDB AlphaHelix', 'PDB-A', 1, 26),
Landmark('PDB AlphaHelix', 'PDB-A', 45, 4)],
list(result))
