def test_rotateby_bad_direction(rotate_universes, direction):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
# what if the box is in the wrong format?
angle = 90
point = [0, 0, 0]
with pytest.raises(ValueError):
rotateby(angle, direction, point=point)(ts)
def test_rotateby_bad_direction(rotate_universes, direction):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
# what if the box is in the wrong format?
angle = 90
point = [0, 0, 0]
with pytest.raises(ValueError):
rotateby(angle, direction, point=point)(ts)
def test_rotateby_bad_point(rotate_universes, point):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
# what if the box is in the wrong format?
angle = 90
vector = [0, 0, 1]
bad_position = point
with pytest.raises(ValueError):
rotateby(angle, vector, point=bad_position)(ts)
def test_rotateby_no_args(rotate_universes):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
angle = 90
vector = [0, 0, 1]
# if no point or AtomGroup are passed to the function
# it should raise a ValueError
with pytest.raises(ValueError):
rotateby(angle, vector)(ts)
def test_rotateby_bad_point(rotate_universes, point):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
# what if the box is in the wrong format?
angle = 90
vector = [0, 0, 1]
bad_position = point
with pytest.raises(ValueError):
rotateby(angle, vector, point=bad_position)(ts)
def test_rotateby_no_args(rotate_universes):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
angle = 90
vector = [0, 0, 1]
# if no point or AtomGroup are passed to the function
# it should raise a ValueError
with pytest.raises(ValueError):
rotateby(angle, vector)(ts)
def test_rotateby_bad_pbc(rotate_universes):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
ag = rotate_universes[0].residues[0].atoms
# is pbc passed to the center methods?
# if yes it should raise an exception for boxes that are zero in size
vector = [1, 0, 0]
angle = 90
with pytest.raises(ValueError):
rotateby(angle, vector, ag=ag, wrap=True)(ts)
def test_rotateby_bad_ag(rotate_universes, ag):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
ag = rotate_universes[0].residues[0].atoms
# what happens if something other than an AtomGroup is given?
angle = 90
vector = [0, 0, 1]
bad_ag = 1
with pytest.raises(ValueError):
rotateby(angle, vector, ag=bad_ag)(ts)
def test_rotateby_no_masses(rotate_universes):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
ag = rotate_universes[0].residues[0].atoms
# if the universe has no masses and `mass` is passed as the center arg
angle = 90
vector = [0, 0, 1]
bad_center = "mass"
with pytest.raises(TypeError):
rotateby(angle, vector, ag=ag, weights=bad_center)(ts)
def test_rotateby_no_masses(rotate_universes):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
ag = rotate_universes[0].residues[0].atoms
# if the universe has no masses and `mass` is passed as the center arg
angle = 90
vector = [0, 0, 1]
bad_center = "mass"
with pytest.raises(TypeError):
rotateby(angle, vector, ag = ag, weights=bad_center)(ts)
def test_rotateby_bad_weights(rotate_universes, weights):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
ag = rotate_universes[0].residues[0].atoms
# what if a wrong center type name is passed?
angle = 90
vector = [0, 0, 1]
bad_weights = " "
with pytest.raises(TypeError):
rotateby(angle, vector, ag = ag, weights=bad_weights)(ts)
def test_rotateby_bad_pbc(rotate_universes):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
ag = rotate_universes[0].residues[0].atoms
# is pbc passed to the center methods?
# if yes it should raise an exception for boxes that are zero in size
vector = [1, 0, 0]
angle = 90
with pytest.raises(ValueError):
rotateby(angle, vector, ag = ag, wrap=True)(ts)
def test_rotateby_bad_ag(rotate_universes, ag):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
ag = rotate_universes[0].residues[0].atoms
# what happens if something other than an AtomGroup is given?
angle = 90
vector = [0, 0, 1]
bad_ag = 1
with pytest.raises(ValueError):
rotateby(angle, vector, ag = bad_ag)(ts)
def test_rotateby_bad_weights(rotate_universes, weights):
# this universe as a box size zero
ts = rotate_universes[0].trajectory.ts
ag = rotate_universes[0].residues[0].atoms
# what if a wrong center type name is passed?
angle = 90
vector = [0, 0, 1]
bad_weights = " "
with pytest.raises(TypeError):
rotateby(angle, vector, ag=ag, weights=bad_weights)(ts)
def test_rotateby_vector(rotate_universes, vector):
# what happens when we use a custom point for the axis of rotation?
ref_u = rotate_universes[0]
trans_u = rotate_universes[1]
trans = trans_u.trajectory.ts
ref = ref_u.trajectory.ts
point = [0, 0, 0]
angle = 90
vec = vector.reshape(3, )
matrix = rotation_matrix(np.deg2rad(angle), vec, point)
ref_u.atoms.transform(matrix)
transformed = rotateby(angle, vector, point=point)(trans)
assert_array_almost_equal(transformed.positions, ref.positions, decimal=6)
def test_rotateby_vector(rotate_universes, vector):
# what happens when we use a custom point for the axis of rotation?
ref_u = rotate_universes[0]
trans_u = rotate_universes[1]
trans = trans_u.trajectory.ts
ref = ref_u.trajectory.ts
point = [0, 0, 0]
angle = 90
vec = vector.reshape(3, )
matrix = rotation_matrix(np.deg2rad(angle), vec, point)
ref_u.atoms.transform(matrix)
transformed = rotateby(angle, vector, point=point)(trans)
assert_array_almost_equal(transformed.positions, ref.positions, decimal=6)
def test_rotateby_atomgroup_cog_nopbc(rotate_universes):
# what happens when we rotate arround the center of geometry of a residue
# without pbc?
ref_u = rotate_universes[0]
trans_u = rotate_universes[1]
trans = trans_u.trajectory.ts
ref = ref_u.trajectory.ts
center_pos = [6, 7, 8]
vector = [1, 0, 0]
angle = 90
matrix = rotation_matrix(np.deg2rad(angle), vector, center_pos)
ref_u.atoms.transform(matrix)
selection = trans_u.residues[0].atoms
transformed = rotateby(angle, vector, ag=selection, weights=None)(trans)
assert_array_almost_equal(transformed.positions, ref.positions, decimal=6)
def test_rotateby_atomgroup_com_pbc(rotate_universes):
# what happens when we rotate arround the center of mass of a residue
# with pbc?
ref_u = rotate_universes[0]
trans_u = rotate_universes[1]
trans = trans_u.trajectory.ts
ref = ref_u.trajectory.ts
vector = [1,0,0]
angle = 90
selection = trans_u.residues[0].atoms
center_pos = selection.center_of_mass(pbc=True)
matrix = rotation_matrix(np.deg2rad(angle), vector, center_pos)
ref_u.atoms.transform(matrix)
transformed = rotateby(angle, vector, ag=selection, weights='mass', wrap=True)(trans)
assert_array_almost_equal(transformed.positions, ref.positions, decimal=6)
def test_rotateby_atomgroup_cog_nopbc(rotate_universes):
# what happens when we rotate arround the center of geometry of a residue
# without pbc?
ref_u = rotate_universes[0]
trans_u = rotate_universes[1]
trans = trans_u.trajectory.ts
ref = ref_u.trajectory.ts
center_pos = [6,7,8]
vector = [1,0,0]
angle = 90
matrix = rotation_matrix(np.deg2rad(angle), vector, center_pos)
ref_u.atoms.transform(matrix)
selection = trans_u.residues[0].atoms
transformed = rotateby(angle, vector, ag=selection, weights=None)(trans)
assert_array_almost_equal(transformed.positions, ref.positions, decimal=6)
def test_rotateby_atomgroup_com_pbc(rotate_universes):
# what happens when we rotate arround the center of mass of a residue
# with pbc?
ref_u = rotate_universes[0]
trans_u = rotate_universes[1]
trans = trans_u.trajectory.ts
ref = ref_u.trajectory.ts
vector = [1, 0, 0]
angle = 90
selection = trans_u.residues[0].atoms
center_pos = selection.center_of_mass(pbc=True)
matrix = rotation_matrix(np.deg2rad(angle), vector, center_pos)
ref_u.atoms.transform(matrix)
transformed = rotateby(angle,
vector,
ag=selection,
weights='mass',
wrap=True)(trans)
assert_array_almost_equal(transformed.positions, ref.positions, decimal=6)
