def testNoExtrema(self):
"""
If an alpha helix has no extrema, the analysis must be as expected.
"""
read = AARead('id', 'GGG')
self.assertEqual(
{
'consecutivePeaks': [],
'consecutiveTroughs': [],
'extremaCount': 0,
'final': None,
'initial': None,
}, analyzeAlphaHelix(read))
def testEmptyRead(self):
"""
The analysis of an empty alpha helix must be as expected.
"""
read = AARead('id', '')
self.assertEqual(
{
'consecutivePeaks': [],
'consecutiveTroughs': [],
'extremaCount': 0,
'final': None,
'initial': None,
}, analyzeAlphaHelix(read))
def testTwoPeaksEachContainingOneAA(self):
"""
If an alpha helix has two peaks, each made up of one amino acid, the
analysis must be as expected.
"""
read = AARead('id', 'GGFGRG')
self.assertEqual(
{
'consecutivePeaks': [1],
'consecutiveTroughs': [1],
'extremaCount': 2,
'final': 1,
'initial': 2,
}, analyzeAlphaHelix(read))
def testOnePeakContainingTwoAAsWithIntermediate(self):
"""
If an alpha helix has one peak made up of two amino acids separated by
a non-peak AA, the analysis must be as expected.
"""
read = AARead('id', 'GFGFGG')
self.assertEqual(
{
'consecutivePeaks': [2],
'consecutiveTroughs': [],
'extremaCount': 2,
'final': 2,
'initial': 1,
}, analyzeAlphaHelix(read))
def testZeroInitialAndFinal(self):
"""
If an alpha helix has no leading non-extrema AAs, the 'initial'
and 'final' values in the analysis must be zero.
"""
read = AARead('id', 'F')
self.assertEqual(
{
'consecutivePeaks': [1],
'consecutiveTroughs': [],
'extremaCount': 1,
'final': 0,
'initial': 0,
}, analyzeAlphaHelix(read))
def testThreePeaksEachContainingMultipleAAsWithIntermediates(self):
"""
If an alpha helix has three peaks, each made up of multiple amino
acids with non-extrema intermediates, the analysis must be as expected.
"""
read = AARead('id', 'GGGFGFFFGRRRGGRRFFGFGGGG')
self.assertEqual(
{
'consecutivePeaks': [4, 3],
'consecutiveTroughs': [5],
'extremaCount': 12,
'final': 4,
'initial': 3,
}, analyzeAlphaHelix(read))