/usr/lib/python2.7/dist-packages/csb/test/cases/bio/io/noe/__init__.py is in python-csb 1.2.2+dfsg-2ubuntu1.
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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 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 | import csb.test as test
import csb.io
from csb.bio.io.noe import SparkyPeakListReader, XeasyPeakListReader, XeasyFileBuilder
from csb.bio.structure import ChemElements
from csb.bio.sequence import ProteinAlphabet
@test.unit
class TestSparkyPeakListReader(test.Case):
def setUp(self):
super(TestSparkyPeakListReader, self).setUp()
self.elements = (ChemElements.H, ChemElements.C, ChemElements.H)
self.parser = SparkyPeakListReader(self.elements, [(1, 2)])
self.file = self.config.getTestFile('Sparky.peaks')
def testRead(self):
content = open(self.file).read()
spectrum = self.parser.read(content)
self.assertEqual(len(spectrum), 3)
self.assertEqual(spectrum.min_intensity, 147454)
self.assertEqual(spectrum.max_intensity, 204746)
self.assertEqual(spectrum.element(0), self.elements[0])
self.assertEqual(spectrum.element(1), self.elements[1])
self.assertEqual(spectrum.dimensions, self.elements)
self.assertEqual(spectrum.proton_dimensions, (0, 2))
self.assertEqual(spectrum.num_dimensions, 3)
self.assertEqual(spectrum.num_proton_dimensions, 2)
self.assertFalse(spectrum.has_element(ChemElements.Ca))
self.assertTrue(spectrum.has_element(ChemElements.C))
self.assertFalse(spectrum.has_connected_dimensions(0))
self.assertEqual(spectrum.connected_dimensions(0), ())
self.assertTrue(spectrum.has_connected_dimensions(1))
self.assertEqual(spectrum.connected_dimensions(1), (2,))
self.assertTrue(spectrum.has_connected_dimensions(2))
self.assertEqual(spectrum.connected_dimensions(2), (1,))
peaks = list(spectrum)
self.assertEqual(peaks[0].intensity, 157921)
self.assertEqual(peaks[0].get(0), 3.418)
self.assertEqual(peaks[0].get(1), 114.437)
self.assertEqual(peaks[0].get(2), 7.440)
def testReadFile(self):
spectrum = self.parser.read_file(self.file)
self.assertEqual(len(spectrum), 3)
def testReadAll(self):
spectrum = self.parser.read_all([self.file, self.file])
self.assertEqual(len(spectrum), 6)
@test.unit
class TestXeasyPeakListReader(test.Case):
def setUp(self):
super(TestXeasyPeakListReader, self).setUp()
self.elements = (ChemElements.H, ChemElements.C, ChemElements.H)
self.parser = XeasyPeakListReader()
self.file = self.config.getTestFile('Xeasy1.peaks')
def testRead(self):
content = open(self.file).read()
spectrum = self.parser.read(content)
self.assertEqual(len(spectrum), 3)
self.assertEqual(spectrum.min_intensity, 1.291120e05)
self.assertEqual(spectrum.max_intensity, 4.243830e05)
self.assertEqual(spectrum.element(0), self.elements[0])
self.assertEqual(spectrum.element(1), self.elements[1])
self.assertEqual(spectrum.dimensions, self.elements)
self.assertEqual(spectrum.proton_dimensions, (0, 2))
self.assertEqual(spectrum.num_dimensions, 3)
self.assertEqual(spectrum.num_proton_dimensions, 2)
self.assertFalse(spectrum.has_element(ChemElements.Ca))
self.assertTrue(spectrum.has_element(ChemElements.C))
self.assertFalse(spectrum.has_connected_dimensions(0))
self.assertEqual(spectrum.connected_dimensions(0), ())
self.assertTrue(spectrum.has_connected_dimensions(1))
self.assertEqual(spectrum.connected_dimensions(1), (2,))
self.assertTrue(spectrum.has_connected_dimensions(2))
self.assertEqual(spectrum.connected_dimensions(2), (1,))
peaks = list(spectrum)
self.assertEqual(peaks[0].intensity, 1.565890e05)
self.assertEqual(peaks[0].get(0), 7.050)
self.assertEqual(peaks[0].get(1), 10.374)
self.assertEqual(peaks[0].get(2), 0.889)
@test.unit
class TestXeasyPeakListReader2(TestXeasyPeakListReader):
def setUp(self):
super(TestXeasyPeakListReader2, self).setUp()
self.elements = (ChemElements.H, ChemElements.C, ChemElements.H)
self.parser = XeasyPeakListReader()
self.file = self.config.getTestFile('Xeasy2.peaks')
@test.unit
class TestXeasyFileBuilder(test.Case):
def setUp(self):
super(TestXeasyFileBuilder, self).setUp()
def testBuild(self):
content = self.config.getContent("Xeasy1.peaks")
spectrum = XeasyPeakListReader().read(content)
stream = csb.io.MemoryStream()
builder = XeasyFileBuilder(stream)
builder.add_header(spectrum)
builder.add_peaks(spectrum)
self.assertEqual(stream.getvalue().strip(), content.strip())
if __name__ == '__main__':
test.Console()
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