def test_cg_rmsd3(self):
cg1 = ftmc.CoarseGrainRNA('test/forgi/threedee/data/1GID_A.cg')
cg2 = ftmc.CoarseGrainRNA('test/forgi/threedee/data/1GID_A.cg')
cg2.coords.rotate(ftuv.rotation_matrix([1.,2.,3.], 22))
cg2.twists.rotate(ftuv.rotation_matrix([1.,2.,3.], 22))
self.assertAlmostEqual(ftme.cg_rmsd(cg1,cg2), 0)
def test_around_xyz(self):
vec = np.array([1., 2., 3.])
nptest.assert_allclose(np.dot(ftuv.rotation_matrix(
"x", math.radians(90)), vec), [1., 3., -2.])
nptest.assert_allclose(np.dot(ftuv.rotation_matrix(
"y", math.radians(90)), vec), [-3., 2., 1.])
nptest.assert_allclose(np.dot(ftuv.rotation_matrix(
"z", math.radians(90)), vec), [2., -1., 3.])
def test_around_xyz(self):
vec = np.array([1., 2., 3.])
nptest.assert_allclose(
np.dot(ftuv.rotation_matrix("x", math.radians(90)), vec),
[1., 3., -2.])
nptest.assert_allclose(
np.dot(ftuv.rotation_matrix("y", math.radians(90)), vec),
[-3., 2., 1.])
nptest.assert_allclose(
np.dot(ftuv.rotation_matrix("z", math.radians(90)), vec),
[2., -1., 3.])
def test_shortcut_works(self):
nptest.assert_allclose(ftuv.rotation_matrix(
"x", 1.3), ftuv.rotation_matrix(ftuv.standard_basis[0], 1.3))
nptest.assert_allclose(ftuv.rotation_matrix(
"y", -2.3), ftuv.rotation_matrix(ftuv.standard_basis[1], -2.3))
nptest.assert_allclose(ftuv.rotation_matrix(
"z", 0.23), ftuv.rotation_matrix(ftuv.standard_basis[2], 0.23))
def test_shortcut_works(self):
nptest.assert_allclose(
ftuv.rotation_matrix("x", 1.3),
ftuv.rotation_matrix(ftuv.standard_basis[0], 1.3))
nptest.assert_allclose(
ftuv.rotation_matrix("y", -2.3),
ftuv.rotation_matrix(ftuv.standard_basis[1], -2.3))
nptest.assert_allclose(
ftuv.rotation_matrix("z", 0.23),
ftuv.rotation_matrix(ftuv.standard_basis[2], 0.23))
def test_rotate_keeps_RMSD_zero(self):
cg1_rot = copy.deepcopy(self.cg1)
cg1_rot.rotate(30, unit="degrees")
# This currently uses virtual atoms, thus takes twists into account.
self.assertLess(ftme.cg_rmsd(self.cg1, cg1_rot), 10**-6)
cg2_rot = copy.deepcopy(self.cg2)
cg2_rot.rotate(45, unit="degrees")
a, b = self.cg2.get_ordered_virtual_residue_poss(True)
log.warning("------------------------")
c, d = cg2_rot.get_ordered_virtual_residue_poss(True)
c2 = np.dot(c, ftuv.rotation_matrix("x", math.radians(-45)).T)
log.warning("==================================")
for i, coord in enumerate(a):
if any(abs(coord - c2[i]) > 10**-4):
log.warning("%s %s %s %s", coord, b[i], c2[i], d[i])
self.assertLess(ftme.cg_rmsd(self.cg2, cg2_rot), 10**-6)
def test_rotate_keeps_RMSD_zero(self):
cg1_rot = copy.deepcopy(self.cg1)
cg1_rot.rotate(30, unit="degrees")
# This currently uses virtual atoms, thus takes twists into account.
self.assertLess(ftme.cg_rmsd(self.cg1, cg1_rot), 10**-6)
cg2_rot = copy.deepcopy(self.cg2)
cg2_rot.rotate(45, unit="degrees")
a,b = self.cg2.get_ordered_virtual_residue_poss(True)
log.warning("------------------------")
c,d = cg2_rot.get_ordered_virtual_residue_poss(True)
c2 = np.dot(c, ftuv.rotation_matrix("x", math.radians(-45)).T)
log.warning("==================================")
for i, coord in enumerate(a):
if any(abs(coord-c2[i])>10**-4):
log.warning("%s %s %s %s",coord, b[i], c2[i], d[i])
self.assertLess(ftme.cg_rmsd(self.cg2, cg2_rot), 10**-6)
def test_list_or_array_works(self):
nptest.assert_allclose(
ftuv.rotation_matrix([2, 3., 4.], 1.43),
ftuv.rotation_matrix(np.array([2, 3., 4.]), 1.43))
def test_special_cases_xyz(self):
nptest.assert_almost_equal(
ftuv.rotation_matrix("x", 0.4),
ftuv.rotation_matrix(ftuv.standard_basis[0], 0.4))
nptest.assert_almost_equal(
ftuv.rotation_matrix("y", 0.7),
ftuv.rotation_matrix(ftuv.standard_basis[1], 0.7))
nptest.assert_almost_equal(
ftuv.rotation_matrix("z", 0.9),
ftuv.rotation_matrix(ftuv.standard_basis[2], 0.9))
nptest.assert_almost_equal(
ftuv.rotation_matrix("x", 1.84),
ftuv.rotation_matrix(ftuv.standard_basis[0], 1.84))
nptest.assert_almost_equal(
ftuv.rotation_matrix("y", 2.7),
ftuv.rotation_matrix(ftuv.standard_basis[1], 2.7))
nptest.assert_almost_equal(
ftuv.rotation_matrix("z", 3.9),
ftuv.rotation_matrix(ftuv.standard_basis[2], 3.9))
def test_special_cases_xyz(self):
nptest.assert_almost_equal(ftuv.rotation_matrix("x", 0.4),
ftuv.rotation_matrix(ftuv.standard_basis[0], 0.4))
nptest.assert_almost_equal(ftuv.rotation_matrix("y", 0.7),
ftuv.rotation_matrix(ftuv.standard_basis[1], 0.7))
nptest.assert_almost_equal(ftuv.rotation_matrix("z", 0.9),
ftuv.rotation_matrix(ftuv.standard_basis[2], 0.9))
nptest.assert_almost_equal(ftuv.rotation_matrix("x", 1.84),
ftuv.rotation_matrix(ftuv.standard_basis[0], 1.84))
nptest.assert_almost_equal(ftuv.rotation_matrix("y", 2.7),
ftuv.rotation_matrix(ftuv.standard_basis[1], 2.7))
nptest.assert_almost_equal(ftuv.rotation_matrix("z", 3.9),
ftuv.rotation_matrix(ftuv.standard_basis[2], 3.9))
def test_list_or_array_works(self):
nptest.assert_allclose(ftuv.rotation_matrix(
[2, 3., 4.], 1.43), ftuv.rotation_matrix(np.array([2, 3., 4.]), 1.43))
def move(self, sm):
self.last_axis = random.choice(["x", "y", "z"])
self.last_angle = random.random()*2*np.pi # 0-360 degrees
rot_mat = ftuv.rotation_matrix(self.last_axis, self.last_angle)
sm.bg.rotate(rot_mat)
return "{}deg{}".format(math.degrees(self.last_angle), self.last_axis)