def test_dihedral():
coord1 = struc.coord([-0.5, -1, 0])
coord2 = struc.coord([0, 0, 0])
coord3 = struc.coord([1, 0, 0])
coord4 = struc.coord([0, 0, -1])
assert struc.dihedral(coord1, coord2, coord3, coord4) \
== pytest.approx(0.5*np.pi)
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 detect_disulfide_bonds(structure,
distance=2.05,
distance_tol=0.05,
dihedral=90,
dihedral_tol=10):
# Array where detected disulfide bonds are stored
disulfide_bonds = []
# A mask that selects only S-gamma atoms of cysteins
sulfide_mask = (structure.res_name == "CYS") & \
(structure.atom_name == "SG")
# sulfides in adjacency to other sulfides are detected in an
# efficient manner via a cell list
cell_list = struc.CellList(structure,
cell_size=distance + distance_tol,
selection=sulfide_mask)
# Iterate over every index corresponding to an S-gamma atom
for sulfide_i in np.where(sulfide_mask)[0]:
# Find indices corresponding to other S-gamma atoms,
# that are adjacent to the position of structure[sulfide_i]
# We use the faster 'get_atoms_in_cells()' instead of
# `get_atoms()`, as precise distance measurement is done
# afterwards anyway
potential_bond_partner_indices = cell_list.get_atoms_in_cells(
coord=structure.coord[sulfide_i])
# Iterate over every index corresponding to an S-gamma atom
# as bond partner
for sulfide_j in potential_bond_partner_indices:
if sulfide_i == sulfide_j:
# A sulfide cannot create a bond with itself:
continue
# Create 'Atom' instances
# of the potentially bonds S-gamma atoms
sg1 = structure[sulfide_i]
sg2 = structure[sulfide_j]
# For dihedral angle measurement the corresponding
# C-beta atoms are required, too
cb1 = structure[(structure.chain_id == sg1.chain_id)
& (structure.res_id == sg1.res_id) &
(structure.atom_name == "CB")]
cb2 = structure[(structure.chain_id == sg2.chain_id)
& (structure.res_id == sg2.res_id) &
(structure.atom_name == "CB")]
# Measure distance and dihedral angle and check criteria
bond_dist = struc.distance(sg1, sg2)
bond_dihed = np.abs(np.rad2deg(struc.dihedral(cb1, sg1, sg2, cb2)))
if bond_dist > distance - distance_tol and \
bond_dist < distance + distance_tol and \
bond_dihed > dihedral - dihedral_tol and \
bond_dihed < dihedral + dihedral_tol:
# Atom meet criteria -> we found a disulfide bond
# -> the indices of the bond S-gamma atoms
# are put into a tuple with the lower index first
bond_tuple = sorted((sulfide_i, sulfide_j))
# Add bond to list of bonds, but each bond only once
if bond_tuple not in disulfide_bonds:
disulfide_bonds.append(bond_tuple)
return np.array(disulfide_bonds, dtype=int)
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
# backbone, :math:`\phi`, :math:`\psi` and :math:`\omega`.
# In the following code snippet we measure these angles and create a
# simple Ramachandran plot for the first frame of *TC5b*.