sup.set(x, y)
# do the qcp fit
sup.run()
# get the rmsd
rms = sup.get_rms()
# get rotation (right multiplying!) and the translation
rot, tran = sup.get_rotran()
# rotate y on x manually
y_on_x1 = dot(y, rot) + tran
# same thing
y_on_x2 = sup.get_transformed()
def simple_matrix_print(matrix):
"""Simple string to display a floating point matrix
This should give the same output on multiple systems. This is
needed because a simple "print matrix" uses scientific notation
which varies between platforms.
Only 4 decimal places are used to avoid false test failures due
to slight differences in the calculation (e.g. due to different
versions of the underlying libraries or the compilation options
they used).
"""
return "[%s]" % "\n ".join("[%s]" % " ".join("% 1.4f" % v for v in row)
class QCPSuperimposerTest(unittest.TestCase):
def setUp(self):
self.x = array([[51.65, -1.90, 50.07], [50.40, -1.23, 50.65],
[50.68, -0.04, 51.54], [50.22, -0.02, 52.85]])
self.y = array([[51.30, -2.99, 46.54], [51.09, -1.88, 47.58],
[52.36, -1.20, 48.03], [52.71, -1.18, 49.38]])
self.sup = QCPSuperimposer()
self.sup.set(self.x, self.y)
# Public methods
def test_set(self):
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3),
around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3),
around(self.y, decimals=3)))
self.assertIsNone(self.sup.transformed_coords)
self.assertIsNone(self.sup.rot)
self.assertIsNone(self.sup.tran)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
def test_run(self):
self.sup.run()
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3),
around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3),
around(self.y, decimals=3)))
self.assertIsNone(self.sup.transformed_coords)
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3),
around(calc_rot, decimals=3)))
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3),
around(calc_tran, decimals=3)))
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.rms), calc_rms)
self.assertIsNone(self.sup.init_rms)
def test_get_transformed(self):
self.sup.run()
transformed_coords = array([[49.05456082, -1.23928381, 50.58427566],
[50.02204971, -0.39367917, 51.42494181],
[51.47738545, -0.57287128, 51.06760944],
[52.39602307, -0.98417088, 52.03318837]])
self.assertTrue(
array_equal(around(self.sup.get_transformed(), decimals=3),
around(transformed_coords, decimals=3)))
def test_get_init_rms(self):
x = array([[1.1, 1.2, 1.3], [1.4, 1.5, 1.6], [1.7, 1.8, 1.9]])
y = array([[1.0, 1.0, 1.0], [1.0, 1.0, 1.0], [1.0, 1.0, 1.0]])
self.sup.set(x, y)
self.assertIsNone(self.sup.init_rms)
init_rms = array([0.81, 0.9, 0.98])
self.assertTrue(
array_equal(around(self.sup.get_init_rms(), decimals=2),
around(init_rms, decimals=2)))
def test_get_rotran(self):
self.sup.run()
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
rot, tran = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot, decimals=3), around(calc_rot, decimals=3)))
self.assertTrue(
array_equal(around(tran, decimals=3), around(calc_tran,
decimals=3)))
def test_get_rms(self):
self.sup.run()
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.get_rms()), calc_rms)
# Old test from Bio/PDB/QCPSuperimposer/__init__.py
def test_oldTest(self):
x = array([[-2.803, -15.373, 24.556], [0.893, -16.062, 25.147],
[1.368, -12.371, 25.885], [-1.651, -12.153, 28.177],
[-0.440, -15.218, 30.068], [2.551, -13.273, 31.372],
[0.105, -11.330, 33.567]])
y = array([[-14.739, -18.673, 15.040], [-12.473, -15.810, 16.074],
[-14.802, -13.307, 14.408], [-17.782, -14.852, 16.171],
[-16.124, -14.617, 19.584], [-15.029, -11.037, 18.902],
[-18.577, -10.001, 17.996]])
self.sup.set(x, y)
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3),
around(x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3),
around(y, decimals=3)))
self.sup.run()
rot = array([[0.72216358, 0.69118937, -0.0271479],
[-0.52038257, 0.51700833, -0.67963547],
[-0.45572112, 0.50493528, 0.73304748]])
tran = array([11.68878393, -4.13245037, 6.05208344])
rms = 0.7191064509622271
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3),
around(rot, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3),
around(tran, decimals=3)))
self.assertEqual(float('%.3f' % self.sup.rms), around(rms, decimals=3))
rms_get = self.sup.get_rms()
self.assertTrue(
array_equal(around(rms_get, decimals=3), around(rms, decimals=3)))
rot_get, tran_get = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot_get, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(tran_get, decimals=3), around(tran,
decimals=3)))
y_on_x1 = dot(y, rot) + tran
y_x_solution = array([[3.90787281, -16.37976032, 30.16808376],
[3.58322456, -12.81122728, 28.91874135],
[1.3580194, -13.96815768, 26.05958411],
[-0.79347336, -15.93647897, 28.48288439],
[-1.27379224, -12.9456459, 30.78004989],
[-2.03519089, -10.6822696, 27.81728956],
[-4.72366028, -13.05646024, 26.54536695]])
self.assertTrue(
array_equal(around(y_on_x1, decimals=3),
around(y_x_solution, decimals=3)))
y_on_x2 = self.sup.get_transformed()
self.assertTrue(
array_equal(around(y_on_x2, decimals=3),
around(y_x_solution, decimals=3)))
sup.set(x, y)
# do the qcp fit
sup.run()
# get the rmsd
rms = sup.get_rms()
# get rotation (right multiplying!) and the translation
rot, tran = sup.get_rotran()
# rotate y on x manually
y_on_x1 = dot(y, rot) + tran
# same thing
y_on_x2 = sup.get_transformed()
def simple_matrix_print(matrix):
"""Simple string to display a floating point matrix
This should give the same output on multiple systems. This is
needed because a simple "print matrix" uses scientific notation
which varies between platforms.
Only 4 decimal places are used to avoid false test failures due
to slight differences in the calculation (e.g. due to different
versions of the underlying libraries or the compilation options
they used).
"""
return "[%s]" % "\n ".join("[%s]" % " ".join("% 1.4f" % v for v in row)
class QCPSuperimposerTest(unittest.TestCase):
def setUp(self):
self.x = array([[51.65, -1.90, 50.07],
[50.40, -1.23, 50.65],
[50.68, -0.04, 51.54],
[50.22, -0.02, 52.85]])
self.y = array([[51.30, -2.99, 46.54],
[51.09, -1.88, 47.58],
[52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]])
self.sup = QCPSuperimposer()
self.sup.set(self.x, self.y)
# Public methods
def test_set(self):
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(self.y, decimals=3)))
self.assertIsNone(self.sup.transformed_coords)
self.assertIsNone(self.sup.rot)
self.assertIsNone(self.sup.tran)
self.assertIsNone(self.sup.rms)
self.assertIsNone(self.sup.init_rms)
def test_run(self):
self.sup.run()
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(self.x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(self.y, decimals=3)))
self.assertIsNone(self.sup.transformed_coords)
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3), around(calc_rot, decimals=3)))
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3), around(calc_tran, decimals=3)))
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.rms), calc_rms)
self.assertIsNone(self.sup.init_rms)
def test_get_transformed(self):
self.sup.run()
transformed_coords = array([[49.05456082, -1.23928381, 50.58427566],
[50.02204971, -0.39367917, 51.42494181],
[51.47738545, -0.57287128, 51.06760944],
[52.39602307, -0.98417088, 52.03318837]])
self.assertTrue(
array_equal(around(self.sup.get_transformed(), decimals=3), around(transformed_coords, decimals=3)))
def test_get_init_rms(self):
x = array([[1.1, 1.2, 1.3],
[1.4, 1.5, 1.6],
[1.7, 1.8, 1.9]])
y = array([[1.0, 1.0, 1.0],
[1.0, 1.0, 1.0],
[1.0, 1.0, 1.0]])
self.sup.set(x, y)
self.assertIsNone(self.sup.init_rms)
init_rms = array([0.81, 0.9, 0.98])
self.assertTrue(
array_equal(around(self.sup.get_init_rms(), decimals=2), around(init_rms, decimals=2)))
def test_get_rotran(self):
self.sup.run()
calc_rot = array([[0.68304939, -0.5227742, -0.51004967],
[0.53664482, 0.83293151, -0.13504605],
[0.49543503, -0.18147239, 0.84947743]])
calc_tran = array([-7.43885125, 36.51522275, 36.81135533])
rot, tran = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot, decimals=3), around(calc_rot, decimals=3)))
self.assertTrue(
array_equal(around(tran, decimals=3), around(calc_tran, decimals=3)))
def test_get_rms(self):
self.sup.run()
calc_rms = 0.003
self.assertEqual(float('%.3f' % self.sup.get_rms()), calc_rms)
# Old test from Bio/PDB/QCPSuperimposer/__init__.py
def test_oldTest(self):
x = array([[-2.803, -15.373, 24.556],
[0.893, -16.062, 25.147],
[1.368, -12.371, 25.885],
[-1.651, -12.153, 28.177],
[-0.440, -15.218, 30.068],
[2.551, -13.273, 31.372],
[0.105, -11.330, 33.567]])
y = array([[-14.739, -18.673, 15.040],
[-12.473, -15.810, 16.074],
[-14.802, -13.307, 14.408],
[-17.782, -14.852, 16.171],
[-16.124, -14.617, 19.584],
[-15.029, -11.037, 18.902],
[-18.577, -10.001, 17.996]])
self.sup.set(x, y)
self.assertTrue(
array_equal(around(self.sup.reference_coords, decimals=3), around(x, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.coords, decimals=3), around(y, decimals=3)))
self.sup.run()
rot = array([[0.72216358, 0.69118937, -0.0271479],
[-0.52038257, 0.51700833, -0.67963547],
[-0.45572112, 0.50493528, 0.73304748]])
tran = array([11.68878393, -4.13245037, 6.05208344])
rms = 0.7191064509622271
self.assertTrue(
array_equal(around(self.sup.rot, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(self.sup.tran, decimals=3), around(tran, decimals=3)))
self.assertEqual(float('%.3f' % self.sup.rms), around(rms, decimals=3))
rms_get = self.sup.get_rms()
self.assertTrue(
array_equal(around(rms_get, decimals=3), around(rms, decimals=3)))
rot_get, tran_get = self.sup.get_rotran()
self.assertTrue(
array_equal(around(rot_get, decimals=3), around(rot, decimals=3)))
self.assertTrue(
array_equal(around(tran_get, decimals=3), around(tran, decimals=3)))
y_on_x1 = dot(y, rot) + tran
y_x_solution = array([[3.90787281, -16.37976032, 30.16808376],
[3.58322456, -12.81122728, 28.91874135],
[1.3580194, -13.96815768, 26.05958411],
[-0.79347336, -15.93647897, 28.48288439],
[-1.27379224, -12.9456459, 30.78004989],
[-2.03519089, -10.6822696, 27.81728956],
[-4.72366028, -13.05646024, 26.54536695]])
self.assertTrue(
array_equal(around(y_on_x1, decimals=3), around(y_x_solution, decimals=3)))
y_on_x2 = self.sup.get_transformed()
self.assertTrue(
array_equal(around(y_on_x2, decimals=3), around(y_x_solution, decimals=3)))