def test_array_conversion(path):
npz_file = npz.NpzFile()
npz_file.read(path)
array1 = npz_file.get_structure()
npz_file = npz.NpzFile()
npz_file.set_structure(array1)
array2 = npz_file.get_structure()
assert array1 == array2
def input_atoms(request):
ndim, as_coord = request.param
file = npz.NpzFile()
file.read(join(data_dir, "1l2y.npz"))
atoms = file.get_structure()
if ndim == 2:
# Only one model
atoms = atoms[0]
elif ndim == 1:
# Only one atom
atoms = atoms[0, 0]
if as_coord:
return atoms.coord
else:
return atoms
def test_dihedral_backbone():
file = npz.NpzFile()
file.read(join(data_dir, "1l2y.npz"))
# Test array
array = file.get_structure()[0]
phi, psi, omega = struc.dihedral_backbone(array, "A")
assert omega.shape == (20, )
# Remove nan values
omega = np.abs(omega)[:-1]
assert omega.tolist() == pytest.approx([np.pi] * len(omega), rel=0.05)
# Test stack
stack = file.get_structure()
phi, psi, omega = struc.dihedral_backbone(stack, "A")
assert omega.shape == (38, 20)
# Remove nan values
omega = np.abs(omega)[:, :-1]
omega = np.average(omega, axis=0)
assert omega.tolist() == pytest.approx([np.pi] * len(omega), rel=0.05)
def array():
file = npz.NpzFile()
file.read(join(data_dir, "1l2y.npz"))
return file.get_structure()[0]
def test_rotate_centered():
file = npz.NpzFile()
file.read(join(data_dir, "1l2y.npz"))
array = file.get_structure()[0]
rotated = struc.rotate_centered(array, [2 * np.pi, 2 * np.pi, 2 * np.pi])
assert np.sum(rotated.coord - array.coord) == pytest.approx(0, abs=1e-4)
# # An alternative file format for storing and loading atom arrays and # stacks even faster, is the *NPZ* format. # The big disadvantage is that the format is *Biotite*-exclusive: # No other software will be able to read these files. # These are simple binary files, that are used to store *NumPy* arrays. # In case of atom arrays and stacks, the annotation arrays and # coordinates are written/read to/from *npz* files via the # :class:`NpzFile` class. # Since no expensive data conversion has to be performed, # this format is the fastest way to save and load atom arrays and # stacks. import biotite.structure.io.npz as npz file = npz.NpzFile() file.set_structure(array) reloaded_array = file.get_structure() ######################################################################## # .. currentmodule:: biotite.structure.io # # Since programmers are usually lazy and do not want to write more code # than necessary, there are two convenient function for loading and # saving atom arrays or stacks, unifying the forementioned file formats: # :func:`load_structure()` takes a file path and outputs an array # (or stack, if the file contains multiple models). # Internally, this function uses the appropriate :class:`File` class, # depending on the file format. # The analogous :func:`save_structure()` function provides a shortcut # for writing to structure files.