def test_index_functions():
"""
The `index_xxx()` functions should give the same result as the
corresponding `xxx` functions.
"""
stack = strucio.load_structure(join(data_dir, "1l2y.mmtf"))
array = stack[0]
# Test for atom array, stack and raw coordinates
samples = (array, stack, struc.coord(array), struc.coord(stack))
# Generate random indices
random.seed(42)
indices = random.randint(array.array_length(), size=(100, 4), dtype=int)
for sample in samples:
if isinstance(sample, np.ndarray):
atoms1 = sample[..., indices[:, 0], :]
atoms2 = sample[..., indices[:, 1], :]
atoms3 = sample[..., indices[:, 2], :]
atoms4 = sample[..., indices[:, 3], :]
else:
atoms1 = sample[..., indices[:, 0]]
atoms2 = sample[..., indices[:, 1]]
atoms3 = sample[..., indices[:, 2]]
atoms4 = sample[..., indices[:, 3]]
assert np.allclose(struc.displacement(atoms1, atoms2),
struc.index_displacement(sample, indices[:, :2]),
atol=1e-5)
assert np.allclose(struc.distance(atoms1, atoms2),
struc.index_distance(sample, indices[:, :2]),
atol=1e-5)
assert np.allclose(struc.angle(atoms1, atoms2, atoms3),
struc.index_angle(sample, indices[:, :3]),
atol=1e-5)
assert np.allclose(struc.dihedral(atoms1, atoms2, atoms3, atoms4),
struc.index_dihedral(sample, indices[:, :4]),
atol=1e-5)
def test_rotate_measure(axis, random_seed):
"""
Rotate and measure resulting angle that should be equal to the input
angle.
"""
np.random.seed(random_seed)
# Maximum rotation is only 180 degrees,
# as with higher angles the measured angle would decrease again
ref_angle = np.random.rand() * np.pi
angles = np.zeros(3)
angles[axis] = ref_angle
# The measured angle is only equal to the input angle,
# if the input coordinates have no component on the rotation axis
input_coord = np.ones(3)
input_coord[axis] = 0
rotated = struc.rotate(input_coord, angles)
test_angle = struc.angle(rotated, 0, input_coord)
# Vector length should be unchanged
assert np.linalg.norm(rotated) \
== pytest.approx(np.linalg.norm(input_coord))
assert test_angle == pytest.approx(ref_angle)
def test_angle():
coord1 = struc.coord([0, 0, 1])
coord2 = struc.coord([0, 0, 0])
coord3 = struc.coord([0, 1, 1])
assert struc.angle(coord1, coord2, coord3) == pytest.approx(0.25 * np.pi)
print(struc.distance(stack, stack[0, 0]).shape)
# And finally distances between two adjacent CA in the first frame
array = stack[0]
print("Adjacent CA distances")
print(struc.distance(array[:-1], array[1:]))
########################################################################
# Like some other functions in :mod:`biotite.structure`, we are able to
# pick any combination of an atom, atom array or stack. Alternatively
# :class:`ndarray` objects containing the coordinates can be provided.
#
# Furthermore, we can measure bond angles and dihedral angles.
# Calculate angle between first 3 CA atoms in first frame
# (in radians)
print("Angle:", struc.angle(array[0], array[1], array[2]))
# Calculate dihedral angle between first 4 CA atoms in first frame
# (in radians)
print("Dihedral angle:", struc.dihedral(array[0], array[1], array[2],
array[4]))
########################################################################
# .. note:: The :func:`distance()`, :func:`angle()` and
# :func:`dihedral()` functions all have their :func:`pair_...()`
# counterparts, that take can atom array (stack) and
# pairs/triplets/quadruplets of atoms, of which distance/angle should
# be calculated.
# Both variants can be setup to consider periodic boundary conditions
# by setting the `box` or `periodic` parameter, respectively.
#
# In some cases one is interested in the dihedral angles of the peptide