def test_dihedral_backbone_result(file_name):
import mdtraj
mmtf_file = mmtf.MMTFFile()
mmtf_file.read(file_name)
array = mmtf.get_structure(mmtf_file, model=1)
array = array[struc.filter_amino_acids(array)]
for chain in struc.chain_iter(array):
print("Chain: ", chain.chain_id[0])
if len(struc.check_id_continuity(chain)) != 0:
# Do not test discontinuous chains
return
test_phi, test_psi, test_ome = struc.dihedral_backbone(chain)
temp_file_name = biotite.temp_file("pdb")
strucio.save_structure(temp_file_name, chain)
traj = mdtraj.load(temp_file_name)
_, ref_phi = mdtraj.compute_phi(traj)
_, ref_psi = mdtraj.compute_psi(traj)
_, ref_ome = mdtraj.compute_omega(traj)
ref_phi, ref_psi, ref_ome = ref_phi[0], ref_psi[0], ref_ome[0]
assert test_phi[1:] == pytest.approx(ref_phi, abs=1e-5, rel=5e-3)
assert test_psi[:-1] == pytest.approx(ref_psi, abs=1e-5, rel=5e-3)
assert test_ome[:-1] == pytest.approx(ref_ome, abs=1e-5, rel=5e-3)
def test_dihedral_backbone_result(file_name):
import mdtraj
mmtf_file = mmtf.MMTFFile.read(file_name)
array = mmtf.get_structure(mmtf_file, model=1)
array = array[struc.filter_amino_acids(array)]
if array.array_length() == 0:
# Structure contains no protein
# -> determination of backbone angles makes no sense
return
for chain in struc.chain_iter(array):
print("Chain: ", chain.chain_id[0])
if len(struc.check_res_id_continuity(chain)) != 0:
# Do not test discontinuous chains
return
test_phi, test_psi, test_ome = struc.dihedral_backbone(chain)
temp = NamedTemporaryFile("w+", suffix=".pdb")
strucio.save_structure(temp.name, chain)
traj = mdtraj.load(temp.name)
temp.close()
_, ref_phi = mdtraj.compute_phi(traj)
_, ref_psi = mdtraj.compute_psi(traj)
_, ref_ome = mdtraj.compute_omega(traj)
ref_phi, ref_psi, ref_ome = ref_phi[0], ref_psi[0], ref_ome[0]
assert test_phi[1:] == pytest.approx(ref_phi, abs=1e-5, rel=5e-3)
assert test_psi[:-1] == pytest.approx(ref_psi, abs=1e-5, rel=5e-3)
assert test_ome[:-1] == pytest.approx(ref_ome, abs=1e-5, rel=5e-3)
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 calculate_dihedral(msaName):
array = pdb2biotite(msaName)
# plt.figure(0)
# plt.plot(phi * 360/(2*np.pi), psi * 360/(2*np.pi),
# marker="o", linestyle="None")
# plt.xlim(-180,180)
# plt.ylim(-180,180)
# plt.xlabel("$\phi$")
# plt.ylabel("$\psi$")
# plt.close()
return struc.dihedral_backbone(array)
def test_dihedral_backbone_general(multiple_chains):
stack = strucio.load_structure(join(data_dir, "1l2y.mmtf"))
n_models = stack.stack_depth()
n_res = stack.res_id[-1]
if multiple_chains:
stack2 = stack.copy()
stack2.chain_id[:] = "B"
stack = stack + stack2
n_res = n_res * 2
array = stack[0]
# Test array
phi, psi, omega = struc.dihedral_backbone(array)
assert phi.shape == (n_res, )
assert psi.shape == (n_res, )
assert omega.shape == (n_res, )
_assert_plausible_omega(omega)
# Test stack
phi, psi, omega = struc.dihedral_backbone(stack)
assert phi.shape == (n_models, n_res)
assert psi.shape == (n_models, n_res)
assert omega.shape == (n_models, n_res)
_assert_plausible_omega(omega)
organisms = ["H. sapiens", "G. gallus", "C. viginianus", "B. mori"]
# Create a PB sequence from each structure
pb_seqs = []
for file_name in lyso_files:
file = mmtf.MMTFFile()
file.read(file_name)
# Take only the first model into account
array = mmtf.get_structure(file, model=1)
# Remove everything but the first protein chain
array = array[struc.filter_amino_acids(array)]
array = array[array.chain_id == array.chain_id[0]]
# Calculate backbone dihedral angles,
# as the PBs are determined from them
phi, psi, omega = struc.dihedral_backbone(array)
# A PB requires the 8 phi/psi angles of 5 amino acids,
# centered on the amino acid to calculate the PB for
# Hence, the PBs are not defined for the two amino acids
# at each terminus
pb_angles = np.full((len(phi) - 4, 8), np.nan)
pb_angles[:, 0] = psi[:-4]
pb_angles[:, 1] = phi[1:-3]
pb_angles[:, 2] = psi[1:-3]
pb_angles[:, 3] = phi[2:-2]
pb_angles[:, 4] = psi[2:-2]
pb_angles[:, 5] = phi[3:-1]
pb_angles[:, 6] = psi[3:-1]
pb_angles[:, 7] = phi[4:]
pb_angles = np.rad2deg(pb_angles)
import biotite
import biotite.structure as struc
import biotite.structure.io as strucio
import biotite.database.rcsb as rcsb
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import colors
import scipy.stats as sts
# Download and parse file
file = rcsb.fetch("3vkh", "cif", biotite.temp_dir())
atom_array = strucio.load_structure(file)
# Calculate backbone dihedral angles
# from one of the two identical chains in the asymmetric unit
phi, psi, omega = struc.dihedral_backbone(
atom_array[atom_array.chain_id == "A"])
# Conversion from radians into degree
phi *= 180 / np.pi
psi *= 180 / np.pi
# Remove invalid values (NaN) at first and last position
phi = phi[1:-1]
psi = psi[1:-1]
# Plot density
figure = plt.figure()
ax = figure.add_subplot(111)
h, xed, yed, image = ax.hist2d(phi,
psi,
bins=(200, 200),
cmap="RdYlGn_r",
cmin=1)
import biotite
import biotite.structure as struc
import biotite.structure.io as strucio
import biotite.database.rcsb as rcsb
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import colors
import scipy.stats as sts
# Download and parse file
file = rcsb.fetch("3vkh", "cif", biotite.temp_dir())
atom_array = strucio.load_structure(file)
# Calculate backbone dihedral angles
# from one of the two identical chains in the asymmetric unit
phi, psi, omega = struc.dihedral_backbone(atom_array, "A")
# Conversion from radians into degree
phi *= 180/np.pi
psi *= 180/np.pi
# Remove invalid values (NaN) at first and last position
phi= phi[1:-1]
psi= psi[1:-1]
# Plot density
figure = plt.figure()
ax = figure.add_subplot(111)
h, xed, yed, image = ax.hist2d(phi, psi, bins=(200, 200),
cmap="RdYlGn_r", cmin=1)
cbar = figure.colorbar(image, orientation="vertical")
cbar.set_label("Count")
ax.set_aspect("equal")
# (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]))
########################################################################
# 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*.
import matplotlib.pyplot as plt
import numpy as np
array = pdbx.get_structure(file, model=1)
phi, psi, omega = struc.dihedral_backbone(array, chain_id="A")
plt.plot(phi * 360/(2*np.pi), psi * 360/(2*np.pi),
marker="o", linestyle="None")
plt.xlim(-180,180)
plt.ylim(-180,180)
plt.xlabel("phi")
plt.ylabel("psi")
plt.show()
########################################################################
# Comparing structures
# ^^^^^^^^^^^^^^^^^^^^
#
# Now we want to calculate a measure of flexibility for each residue in
# *TC5b*. The *root mean square fluctuation* (RMSF) is a good value for
# that.
