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))