def test_chain_len_groups(self):
chain_len_map = {'A': 1, 'C': 3, 'B': 2, 'E': 3, 'D': 2}
expected = {1: ['A'], 2: ['B', 'D'], 3: ['C', 'E']}
self.assertDictEqual(
expected,
ChainMappingRMSDMatrixCalculator.getChainLenGroups(chain_len_map))
self.assertItemsEqual(
[['A'], ['B', 'D'], ['C', 'E']],
ChainMappingRMSDMatrixCalculator.getPermGroups(
ChainMappingRMSDMatrixCalculator.getChainLenGroups(
chain_len_map)))
def test_reorderAllCoordinatesByChainLen(self):
input = StringIO.StringIO(chain_padding_proto_3)
structure = prody.parsePDBStream(input)
group_lens = {1: ['A'], 2: ['B', 'D'], 3: ['C', 'E']}
result = ChainMappingRMSDMatrixCalculator.getReorderedCoordinatesByLenGroups(structure, "all", group_lens)
expected =[[[1.0, 2.0, 3.0],
[4.0, 5.0, 6.0],
[7.0, 8.0, 9.0],
[19.0, 20.0, 21.0],
[22.0, 23.0, 24.0],
[10.0, 11.0, 12.0],
[13.0, 14.0, 15.0],
[16.0, 17.0, 18.0],
[25.0, 26.0, 27.0],
[28.0, 29.0, 30.0],
[31.0, 32.0, 33.0]],
[[41.0, 42.0, 43.0],
[44.0, 45.0, 46.0],
[47.0, 48.0, 49.0],
[59.0, 60.0, 61.0],
[62.0, 63.0, 64.0],
[50.0, 51.0, 52.0],
[53.0, 54.0, 55.0],
[56.0, 57.0, 58.0],
[65.0, 66.0, 67.0],
[68.0, 69.0, 70.0],
[71.0, 72.0, 73.0]]]
numpy.testing.assert_array_equal(expected, result)
def test_getStructureChains(self):
expected = [{
'A': numpy.array([[1., 2., 3.]]),
'X': numpy.array([[-33.115, 1.294, -1.163]])
}, {
'A': numpy.array([[4., 5., 6.]]),
'X': numpy.array([[-32.555, -2.5, -5.367]])
}, {
'A': numpy.array([[7., 8., 9.]]),
'X': numpy.array([[-33.257, 5.28, -8.441]])
}, {
'A': numpy.array([[10., 11., 12.]]),
'X': numpy.array([[32.306, 6.517, -1.544]])
}, {
'A': numpy.array([[13., 14., 15.]]),
'X': numpy.array([[30.494, 10.39, -3.066]])
}]
input = StringIO.StringIO(pdb_data)
pdb_structure = prody.parsePDBStream(input)
result = ChainMappingRMSDMatrixCalculator.getStructureChains(
pdb_structure, "all")
for i in range(len(expected)):
numpy.testing.assert_array_equal(expected[i]['A'], result[i]['A'])
numpy.testing.assert_array_equal(expected[i]['X'], result[i]['X'])
def test_getChainLengths(self):
input = StringIO.StringIO(chain_padding_proto_3)
structure = prody.parsePDBStream(input)
self.assertDictEqual({
'A': 1,
'C': 3,
'B': 2,
'E': 3,
'D': 2
}, ChainMappingRMSDMatrixCalculator.getChainLengths(structure, "all"))
def test_reorderCoordinates(self):
chain = {
'A': numpy.array([[1., 2., 3.]]),
'X': numpy.array([[-33.115, 1.294, -1.163]])
}
chain_map = {"A": "X", "X": "A"}
numpy.testing.assert_array_equal(
[[-33.115, 1.294, -1.163], [1., 2., 3.]],
ChainMappingRMSDMatrixCalculator.reorderCoordinates(
chain, ["X", "A"]))
def test_getStructureChains(self):
expected = [{'A': numpy.array([[ 1., 2., 3.]]), 'X': numpy.array([[-33.115, 1.294, -1.163]])},
{'A': numpy.array([[ 4., 5., 6.]]), 'X': numpy.array([[-32.555, -2.5 , -5.367]])},
{'A': numpy.array([[ 7., 8., 9.]]), 'X': numpy.array([[-33.257, 5.28 , -8.441]])},
{'A': numpy.array([[ 10., 11., 12.]]), 'X': numpy.array([[ 32.306, 6.517, -1.544]])},
{'A': numpy.array([[ 13., 14., 15.]]), 'X': numpy.array([[ 30.494, 10.39 , -3.066]])}]
input = StringIO.StringIO(pdb_data)
pdb_structure = prody.parsePDBStream(input)
result = ChainMappingRMSDMatrixCalculator.getStructureChains(pdb_structure,"all")
for i in range(len(expected)):
numpy.testing.assert_array_equal(expected[i]['A'], result[i]['A'])
numpy.testing.assert_array_equal(expected[i]['X'], result[i]['X'])
def test_reorderAllCoordinatesByChainLen(self):
input = StringIO.StringIO(chain_padding_proto_3)
structure = prody.parsePDBStream(input)
group_lens = {1: ['A'], 2: ['B', 'D'], 3: ['C', 'E']}
result = ChainMappingRMSDMatrixCalculator.getReorderedCoordinatesByLenGroups(
structure, "all", group_lens)
expected = [[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0],
[19.0, 20.0, 21.0], [22.0, 23.0,
24.0], [10.0, 11.0, 12.0],
[13.0, 14.0, 15.0], [16.0, 17.0,
18.0], [25.0, 26.0, 27.0],
[28.0, 29.0, 30.0], [31.0, 32.0, 33.0]],
[[41.0, 42.0, 43.0], [44.0, 45.0,
46.0], [47.0, 48.0, 49.0],
[59.0, 60.0, 61.0], [62.0, 63.0,
64.0], [50.0, 51.0, 52.0],
[53.0, 54.0, 55.0], [56.0, 57.0,
58.0], [65.0, 66.0, 67.0],
[68.0, 69.0, 70.0], [71.0, 72.0, 73.0]]]
numpy.testing.assert_array_equal(expected, result)
def test_chain_len_groups(self):
chain_len_map = {'A': 1, 'C': 3, 'B': 2, 'E': 3, 'D': 2}
expected = {1: ['A'], 2: ['B', 'D'], 3: ['C', 'E']}
self.assertDictEqual(expected, ChainMappingRMSDMatrixCalculator.getChainLenGroups(chain_len_map))
self.assertItemsEqual([['A'], ['B', 'D'], ['C', 'E']], ChainMappingRMSDMatrixCalculator.getPermGroups(ChainMappingRMSDMatrixCalculator.getChainLenGroups(chain_len_map)))
def test_getChainLengths(self):
input = StringIO.StringIO(chain_padding_proto_3)
structure = prody.parsePDBStream(input)
self.assertDictEqual({'A': 1, 'C': 3, 'B': 2, 'E': 3, 'D': 2},
ChainMappingRMSDMatrixCalculator.getChainLengths(structure, "all"))
def test_reorderCoordinates(self):
chain = {'A': numpy.array([[ 1., 2., 3.]]), 'X': numpy.array([[-33.115, 1.294, -1.163]])}
chain_map = {"A":"X", "X":"A"}
numpy.testing.assert_array_equal( [[-33.115, 1.294, -1.163], [ 1., 2., 3.]],
ChainMappingRMSDMatrixCalculator.reorderCoordinates(chain, ["X","A"]))
