def test_align_vectors(input_atoms, as_list, use_support, random_seed):
"""
Align, swap alignment vectors and align again.
Expect that the original coordinates have been restored.
"""
np.random.seed(random_seed)
source_direction = np.random.rand(3)
target_direction = np.random.rand(3)
if use_support:
source_position = np.random.rand(3)
target_position = np.random.rand(3)
else:
source_position = None
target_position = None
if as_list:
source_direction = source_direction.tolist()
target_direction = target_direction.tolist()
if use_support:
source_position = source_position.tolist()
target_position = target_position.tolist()
transformed = struc.align_vectors(input_atoms, source_direction,
target_direction, source_position,
target_position)
restored = struc.align_vectors(transformed, target_direction,
source_direction, target_position,
source_position)
assert type(restored) == type(input_atoms)
assert struc.coord(restored).shape == struc.coord(input_atoms).shape
assert np.allclose(struc.coord(restored),
struc.coord(input_atoms),
atol=1e-5)
def test_align_vectors_non_vector_inputs(input_atoms):
"""
Ensure input vectors to ``struct.align_vectors`` have the correct shape.
"""
source_direction = np.random.rand(2, 3)
target_direction = np.random.rand(2, 3)
with pytest.raises(ValueError):
struc.align_vectors(
input_atoms,
source_direction,
target_direction,
)
source_direction = np.random.rand(4)
target_direction = np.random.rand(4)
with pytest.raises(ValueError):
struc.align_vectors(
input_atoms,
source_direction,
target_direction,
)
RAY_ALPHA = 0.03 # The color map to use to depict the charge CMAP_NAME = "bwr_r" # Get an atom array for the selected molecule molecule = info.residue(MOLECULE_NAME) # Align molecule with principal component analysis: # The component with the least variance, i.e. the axis with the lowest # number of atoms lying over each other, is aligned to the z-axis, # which points into the plane of the figure pca = PCA(n_components=3) pca.fit(molecule.coord) molecule = struc.align_vectors(molecule, pca.components_[-1], [0, 0, 1]) # Balls should be colored by partial charge charges = struc.partial_charges(molecule, ITERATION_NUMBER) # Later this variable stores values between 0 and 1 for use in color map normalized_charges = charges.copy() # Show no partial charge for atoms # that are not parametrized for the PEOE algorithm normalized_charges[np.isnan(normalized_charges)] = 0 # Norm charge values to highest absolute value max_charge = np.max(np.abs(normalized_charges)) normalized_charges /= max_charge # Transform range (-1, 1) to range (0, 1) normalized_charges = (normalized_charges + 1) / 2 # Calculate colors color_map = plt.get_cmap(CMAP_NAME)
in struc.get_residue_masks(nucleotides, [i, j])]
break
pairs = [(guanine, cytosine), (adenine, thymine)]
fig = plt.figure(figsize=(8.0, 8.0))
ax = fig.add_subplot(111, projection="3d")
# Arrange bases
for i, (purine, pyrimidine) in enumerate(pairs):
n1, n3, c5, c6 = [pyrimidine[pyrimidine.atom_name == name][0]
for name in ("N1", "N3", "C5", "C6")]
# Pyrimidine N3-C6 axis is aligned to x-axis
purine, pyrimidine = [
struc.align_vectors(
base,
n3.coord - c6.coord,
np.array([1, 0, 0])
) for base in (purine, pyrimidine)
]
# Coords are changed -> update 'Atom' objects
n1, n3, c4, c5 = [pyrimidine[pyrimidine.atom_name == name][0]
for name in ("N1", "N3", "C4", "C5")]
# Pyrimidine base plane normal vector is aligned to z-axis
# Furthermore, distance between bases is set
purine, pyrimidine = [
struc.align_vectors(
base,
np.cross(n3.coord - n1.coord, c5.coord - n1.coord),
np.array([0, 0, 1]),
origin_position = struc.centroid(purine + pyrimidine),
# 10 Å separation between pairs
import biotite.structure as struc
import biotite.structure.info as info
import biotite.structure.graphics as graphics
# Get an atom array for caffeine
# Caffeine has the PDB reside name 'CFF'
caffeine = info.residue("CFF")
# For cosmetic purposes align central rings to x-y plane
n1 = caffeine[caffeine.atom_name == "N1"][0]
n3 = caffeine[caffeine.atom_name == "N3"][0]
n7 = caffeine[caffeine.atom_name == "N7"][0]
# Normal vector of ring plane
normal = np.cross(n1.coord - n3.coord, n1.coord - n7.coord)
# Align ring plane normal to z-axis
caffeine = struc.align_vectors(caffeine, normal, np.array([0, 0, 1]))
# Caffeine should be colored by element
colors = np.zeros((caffeine.array_length(), 3))
colors[caffeine.element == "H"] = (0.8, 0.8, 0.8) # gray
colors[caffeine.element == "C"] = (0.0, 0.8, 0.0) # green
colors[caffeine.element == "N"] = (0.0, 0.0, 0.8) # blue
colors[caffeine.element == "O"] = (0.8, 0.0, 0.0) # red
fig = plt.figure(figsize=(8.0, 8.0))
ax = fig.add_subplot(111, projection="3d")
graphics.plot_atoms(ax,
caffeine,
colors,
line_width=5,
background_color="white",