/usr/lib/python3/dist-packages/csb/test/cases/bio/io/cs/__init__.py is in python3-csb 1.2.2+dfsg-2ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | import csb.test as test
from csb.bio.io.cs import ChemShiftReader, ChemShift3Reader, ChemShiftFormatError
from csb.bio.structure import ChemElements
from csb.bio.sequence import ProteinAlphabet
@test.unit
class TestChemShiftReader(test.Case):
def setUp(self):
super(TestChemShiftReader, self).setUp()
self.parser = self.klass()
self.file2 = self.config.getTestFile('2l01.v2.str')
self.file3 = self.config.getTestFile('2l01.v3.str')
@property
def file(self):
return self.file2
@property
def klass(self):
return ChemShiftReader
def testCreate(self):
klass = self.klass
self.assertTrue(isinstance(klass.create(version=2), ChemShiftReader))
self.assertTrue(isinstance(klass.create(version=3), ChemShift3Reader))
self.assertRaises(ValueError, klass.create, version=1)
def testGuess(self):
klass = self.klass
self.assertTrue(isinstance(klass.guess(self.file2), ChemShiftReader))
self.assertTrue(isinstance(klass.guess(self.file3), ChemShift3Reader))
dummy = self.config.getTestFile("2JZC.sum")
self.assertRaises(ChemShiftFormatError, klass.guess, dummy)
def testReadShifts(self):
content = open(self.file).read()
cs = self.parser.read_shifts(content)
self.assertEqual(len(cs), 11)
self.assertEqual(cs[0].name, "HA")
self.assertEqual(cs[0].element, ChemElements.H)
self.assertEqual(cs[0].shift, 3.977)
self.assertEqual(cs[1].name, "HB2")
self.assertEqual(cs[1].shift, 2.092)
self.assertEqual(cs[7].element, ChemElements.C)
self.assertEqual(cs[7].residue, ProteinAlphabet.MET)
self.assertEqual(cs[10].residue, ProteinAlphabet.LYS)
self.assertEqual(cs[10].shift, 4.423)
def testReadFile(self):
cs = self.parser.read_file(self.file)
self.assertEqual(len(cs), 11)
@test.unit
class TestChemShift3Reader(TestChemShiftReader):
@property
def file(self):
return self.file3
@property
def klass(self):
return ChemShift3Reader
if __name__ == '__main__':
test.Console()
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