def test_loop_exp_frq_offset_cpmg(self):
"""Unit test of the loop_exp_frq_offset() function.
This uses the data of the saved state attached to U{bug #21665<https://gna.org/bugs/?21665>}.
"""
# Load the state.
statefile = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2'
state.load_state(statefile, force=True)
# Original data (exp_type, frq, offset).
data = [
['SQ CPMG', 499862140.0, 0],
['SQ CPMG', 599890858.69999993, 0]
]
# Original indices (ei, mi, oi).
indices = [
[0, 0, 0],
[0, 1, 0]
]
# Check the number of iterations.
print("Checking the number of iterations of the loop.")
count = 0
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(return_indices=True):
print(exp_type, frq, offset, ei, mi, oi)
count += 1
self.assertEqual(count, 2)
# Check the values.
print("Checking the values returned by the loop.")
index = 0
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(return_indices=True):
# Check the experiment info.
self.assertEqual(exp_type, data[index][0])
self.assertEqual(ei, indices[index][0])
# Check the frequency info.
self.assertEqual(frq, data[index][1])
self.assertEqual(mi, indices[index][1])
# Check the offset info.
self.assertEqual(offset, data[index][2])
self.assertEqual(oi, indices[index][2])
# Increment the data index.
index += 1
def test_loop_exp_frq_offset_cpmg(self):
"""Unit test of the loop_exp_frq_offset() function.
This uses the data of the saved state attached to U{bug #21665<https://web.archive.org/web/https://gna.org/bugs/?21665>}.
"""
# Load the state.
statefile = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'dispersion' + sep + 'bug_21665.bz2'
state.load_state(statefile, force=True)
# Original data (exp_type, frq, offset).
data = [['SQ CPMG', 499862140.0, 0],
['SQ CPMG', 599890858.69999993, 0]]
# Original indices (ei, mi, oi).
indices = [[0, 0, 0], [0, 1, 0]]
# Check the number of iterations.
print("Checking the number of iterations of the loop.")
count = 0
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(
return_indices=True):
print(exp_type, frq, offset, ei, mi, oi)
count += 1
self.assertEqual(count, 2)
# Check the values.
print("Checking the values returned by the loop.")
index = 0
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(
return_indices=True):
# Check the experiment info.
self.assertEqual(exp_type, data[index][0])
self.assertEqual(ei, indices[index][0])
# Check the frequency info.
self.assertEqual(frq, data[index][1])
self.assertEqual(mi, indices[index][1])
# Check the offset info.
self.assertEqual(offset, data[index][2])
self.assertEqual(oi, indices[index][2])
# Increment the data index.
index += 1
def generate_theta_dic():
# Get the field count
field_count = cdp.spectrometer_frq_count
# Get the spin_lock_field points
spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
# Initialize data containers
all_spin_ids = get_spin_ids()
# Containers for only selected spins
cur_spin_ids = []
cur_spins = []
for curspin_id in all_spin_ids:
# Get the spin
curspin = return_spin(spin_id=curspin_id)
# Check if is selected
if curspin.select == True:
cur_spin_ids.append(curspin_id)
cur_spins.append(curspin)
# The offset and R1 data.
chemical_shifts, offsets, tilt_angles, Delta_omega, w_eff = return_offset_data(spins=cur_spins, spin_ids=cur_spin_ids, field_count=field_count, fields=spin_lock_nu1)
# Loop over the index of spins, then exp_type, frq, offset
print("Printing the following")
print("exp_type curspin_id frq offset{ppm} offsets[ei][si][mi][oi]{rad/s} ei mi oi si di cur_spin.chemical_shift{ppm} chemical_shifts[ei][si][mi]{rad/s} spin_lock_nu1{Hz} tilt_angles[ei][si][mi][oi]{rad}")
for si in range(len(cur_spin_ids)):
theta_spin_dic = dict()
curspin_id = cur_spin_ids[si]
cur_spin = cur_spins[si]
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(return_indices=True):
# Loop over the dispersion points.
spin_lock_fields = spin_lock_nu1[ei][mi][oi]
for di in range(len(spin_lock_fields)):
print("%-8s %-10s %11.1f %8.4f %12.5f %i %i %i %i %i %7.3f %12.5f %12.5f %12.5f"%(exp_type, curspin_id, frq, offset, offsets[ei][si][mi][oi], ei, mi, oi, si, di, cur_spin.chemical_shift, chemical_shifts[ei][si][mi], spin_lock_fields[di], tilt_angles[ei][si][mi][oi][di]))
dic_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=spin_lock_fields[di])
theta_spin_dic["%s"%(dic_key)] = tilt_angles[ei][si][mi][oi][di]
# Store the data
cur_spin.theta = theta_spin_dic
print("\nThe theta data now resides in")
for curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
spin_index = find_index(selection=spin_id, global_index=False)
print("%s cdp.mol[%i].res[%i].spin[%i].theta"%(spin_id, spin_index[0], spin_index[1], spin_index[2]))
def generate_theta_dic():
# Get the field count
field_count = cdp.spectrometer_frq_count
# Get the spin_lock_field points
spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
# Initialize data containers
all_spin_ids = get_spin_ids()
# Containers for only selected spins
cur_spin_ids = []
cur_spins = []
for curspin_id in all_spin_ids:
# Get the spin
curspin = return_spin(curspin_id)
# Check if is selected
if curspin.select == True:
cur_spin_ids.append(curspin_id)
cur_spins.append(curspin)
# The offset and R1 data.
chemical_shifts, offsets, tilt_angles, Delta_omega, w_eff = return_offset_data(spins=cur_spins, spin_ids=cur_spin_ids, field_count=field_count, fields=spin_lock_nu1)
# Loop over the index of spins, then exp_type, frq, offset
print("Printing the following")
print("exp_type curspin_id frq offset{ppm} offsets[ei][si][mi][oi]{rad/s} ei mi oi si di cur_spin.chemical_shift{ppm} chemical_shifts[ei][si][mi]{rad/s} spin_lock_nu1{Hz} tilt_angles[ei][si][mi][oi]{rad}")
for si in range(len(cur_spin_ids)):
theta_spin_dic = dict()
curspin_id = cur_spin_ids[si]
cur_spin = cur_spins[si]
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(return_indices=True):
# Loop over the dispersion points.
spin_lock_fields = spin_lock_nu1[ei][mi][oi]
for di in range(len(spin_lock_fields)):
print("%-8s %-10s %11.1f %8.4f %12.5f %i %i %i %i %i %7.3f %12.5f %12.5f %12.5f"%(exp_type, curspin_id, frq, offset, offsets[ei][si][mi][oi], ei, mi, oi, si, di, cur_spin.chemical_shift, chemical_shifts[ei][si][mi], spin_lock_fields[di], tilt_angles[ei][si][mi][oi][di]))
dic_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=spin_lock_fields[di])
theta_spin_dic["%s"%(dic_key)] = tilt_angles[ei][si][mi][oi][di]
# Store the data
cur_spin.theta = theta_spin_dic
print("\nThe theta data now resides in")
for curspin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
spin_index = find_index(selection=spin_id, global_index=False)
print("%s cdp.mol[%i].res[%i].spin[%i].theta"%(spin_id, spin_index[0], spin_index[1], spin_index[2]))
def _assemble_cpmg_data(self, spin_id=None):
"""Assemble the CPMG data.
@keyword spin_id: The spin ID string to restrict data to.
@type spin_id: str
"""
# Spin loop.
for spin, mol_name, res_num, res_name, id in spin_loop(full_info=True, selection=spin_id, return_id=True, skip_desel=True):
# The residue index.
res_index = res_num - 1
# Sanity checks.
if res_index < 0:
raise RelaxError("A residue number of less than 1 is not supported in NESSY.")
elif res_index > 699:
raise RelaxError("A residue number of greater than 700 is not supported in NESSY.")
# Loop over all spectrometer frequencies.
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(return_indices=True):
# Loop over all dispersion points.
di_new = 0
for point, di in loop_point(exp_type=exp_type, frq=frq, offset=offset, skip_ref=False, return_indices=True):
# The keys.
keys = find_intensity_keys(exp_type=exp_type, frq=frq, point=point, time=cdp.relax_time_list[0])
# Convert the reference point for NESSY input.
if point == None or isNaN(point):
point = 0
# Loop over the keys.
for key in keys:
# Another check.
if self.cpmg_data[mi][di_new][res_index] != '':
raise RelaxError("Only one spin system per residue is supported in NESSY.")
# Store the data (if it exists).
if key in spin.peak_intensity:
self.cpmg_data[mi][di_new][res_index] = str(spin.peak_intensity[key])
# The CPMG frequency.
self.cpmg_frqs[mi][di_new] = str(point)
# Increment the field index.
di_new += 1
def test_return_offset_data(self):
"""Unit test of the return_offset_data() function for R1rho setup.
This uses the data of the saved state attached to U{bug #21344<https://gna.org/bugs/?21344>}.
"""
# Load the state.
statefile = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344_trunc.bz2'
state.load_state(statefile, force=True)
# Get the field count
field_count = cdp.spectrometer_frq_count
# Get the spin_lock_field points
spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
# Initialize data containers
all_spin_ids = get_spin_ids()
# Containers for only selected spins
cur_spin_ids = []
cur_spins = []
for curspin_id in all_spin_ids:
# Get the spin
curspin = return_spin(curspin_id)
# Check if is selected
if curspin.select == True:
cur_spin_ids.append(curspin_id)
cur_spins.append(curspin)
# Get the spectometer frequency
sfrq = cdp.spectrometer_frq_list[0]
# Gyromagnetic ratios
g1H = 26.7522212 * 1e7
g15N = -2.7126 * 1e7
# The offset and R1 data.
offsets, spin_lock_fields_inter, chemical_shifts, tilt_angles, Delta_omega, w_eff = return_offset_data(spins=cur_spins, spin_ids=cur_spin_ids, field_count=field_count, fields=spin_lock_nu1)
# Loop over the index of spins, then exp_type, frq, offset
print("Printing the following")
print("exp_type curspin_id frq offset{ppm} offsets[ei][si][mi][oi]{rad/s} ei mi oi si di cur_spin.chemical_shift{ppm} chemical_shifts[ei][si][mi]{rad/s} spin_lock_nu1{Hz} tilt_angles[ei][si][mi][oi]{rad}")
for si in range(len(cur_spin_ids)):
curspin_id = cur_spin_ids[si]
cur_spin = cur_spins[si]
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(return_indices=True):
# Loop over the dispersion points.
spin_lock_fields = spin_lock_nu1[ei][mi][oi]
for di in range(len(spin_lock_fields)):
print("%-8s %-10s %11.1f %8.4f %12.5f %i %i %i %i %i %7.3f %12.5f %12.5f %12.5f"%(exp_type, curspin_id, frq, offset, offsets[ei][si][mi][oi], ei, mi, oi, si, di, cur_spin.chemical_shift, chemical_shifts[ei][si][mi], spin_lock_fields[di], tilt_angles[ei][si][mi][oi][di]))
# Test chemical shift conversion
self.assertEqual(chemical_shifts[ei][si][mi], cur_spin.chemical_shift * 2.0 * pi * sfrq / g1H * g15N * 1e-6)
# Test the offset conversion
self.assertEqual(offsets[ei][si][mi][oi], offset * 2.0 * pi * sfrq / g1H * g15N * 1e-6)
# Test the tiltangle
c_omega1 = spin_lock_fields[di] * 2.0 * pi
c_Delta_omega = chemical_shifts[ei][si][mi] - offsets[ei][si][mi][oi]
if c_omega1 / c_Delta_omega > 0:
c_theta = atan(c_omega1 / c_Delta_omega)
else:
c_theta = pi + atan(c_omega1 / c_Delta_omega)
self.assertAlmostEqual(tilt_angles[ei][si][mi][oi][di], c_theta, 15)
def test_return_offset_data(self):
"""Unit test of the return_offset_data() function for R1rho setup.
This uses the data of the saved state attached to U{bug #21344<https://web.archive.org/web/https://gna.org/bugs/?21344>}.
"""
# Load the state.
statefile = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'dispersion' + sep + 'bug_21344_trunc.bz2'
state.load_state(statefile, force=True)
# Get the field count
field_count = cdp.spectrometer_frq_count
# Get the spin_lock_field points
spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
# Initialize data containers
all_spin_ids = get_spin_ids()
# Containers for only selected spins
cur_spin_ids = []
cur_spins = []
for curspin_id in all_spin_ids:
# Get the spin
curspin = return_spin(spin_id=curspin_id)
# Check if is selected
if curspin.select == True:
cur_spin_ids.append(curspin_id)
cur_spins.append(curspin)
# Get the spectometer frequency
sfrq = cdp.spectrometer_frq_list[0]
# Gyromagnetic ratios
g1H = 26.7522212 * 1e7
g15N = -2.7126 * 1e7
# The offset and R1 data.
offsets, spin_lock_fields_inter, chemical_shifts, tilt_angles, Delta_omega, w_eff = return_offset_data(
spins=cur_spins,
spin_ids=cur_spin_ids,
field_count=field_count,
fields=spin_lock_nu1)
# Loop over the index of spins, then exp_type, frq, offset
print("Printing the following")
print(
"exp_type curspin_id frq offset{ppm} offsets[ei][si][mi][oi]{rad/s} ei mi oi si di cur_spin.chemical_shift{ppm} chemical_shifts[ei][si][mi]{rad/s} spin_lock_nu1{Hz} tilt_angles[ei][si][mi][oi]{rad}"
)
for si in range(len(cur_spin_ids)):
curspin_id = cur_spin_ids[si]
cur_spin = cur_spins[si]
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(
return_indices=True):
# Loop over the dispersion points.
spin_lock_fields = spin_lock_nu1[ei][mi][oi]
for di in range(len(spin_lock_fields)):
print(
"%-8s %-10s %11.1f %8.4f %12.5f %i %i %i %i %i %7.3f %12.5f %12.5f %12.5f"
% (exp_type, curspin_id, frq, offset,
offsets[ei][si][mi][oi], ei, mi, oi, si, di,
cur_spin.chemical_shift,
chemical_shifts[ei][si][mi], spin_lock_fields[di],
tilt_angles[ei][si][mi][oi][di]))
# Test chemical shift conversion
self.assertEqual(
chemical_shifts[ei][si][mi], cur_spin.chemical_shift *
2.0 * pi * sfrq / g1H * g15N * 1e-6)
# Test the offset conversion
self.assertEqual(
offsets[ei][si][mi][oi],
offset * 2.0 * pi * sfrq / g1H * g15N * 1e-6)
# Test the tiltangle
c_omega1 = spin_lock_fields[di] * 2.0 * pi
c_Delta_omega = chemical_shifts[ei][si][mi] - offsets[ei][
si][mi][oi]
if c_omega1 / c_Delta_omega > 0:
c_theta = atan(c_omega1 / c_Delta_omega)
else:
c_theta = pi + atan(c_omega1 / c_Delta_omega)
self.assertAlmostEqual(tilt_angles[ei][si][mi][oi][di],
c_theta, 15)
def _assemble_cpmg_data(self, spin_id=None):
"""Assemble the CPMG data.
@keyword spin_id: The spin ID string to restrict data to.
@type spin_id: str
"""
# Spin loop.
for spin, mol_name, res_num, res_name, id in spin_loop(
full_info=True, selection=spin_id, return_id=True,
skip_desel=True):
# The residue index.
res_index = res_num - 1
# Sanity checks.
if res_index < 0:
raise RelaxError(
"A residue number of less than 1 is not supported in NESSY."
)
elif res_index > 699:
raise RelaxError(
"A residue number of greater than 700 is not supported in NESSY."
)
# Loop over all spectrometer frequencies.
for exp_type, frq, offset, ei, mi, oi in loop_exp_frq_offset(
return_indices=True):
# Loop over all dispersion points.
di_new = 0
for point, di in loop_point(exp_type=exp_type,
frq=frq,
offset=offset,
skip_ref=False,
return_indices=True):
# The keys.
keys = find_intensity_keys(exp_type=exp_type,
frq=frq,
point=point,
time=cdp.relax_time_list[0])
# Convert the reference point for NESSY input.
if point == None or isNaN(point):
point = 0
# Loop over the keys.
for key in keys:
# Another check.
if self.cpmg_data[mi][di_new][res_index] != '':
raise RelaxError(
"Only one spin system per residue is supported in NESSY."
)
# Store the data (if it exists).
if key in spin.peak_intensity:
self.cpmg_data[mi][di_new][res_index] = str(
spin.peak_intensity[key])
# The CPMG frequency.
self.cpmg_frqs[mi][di_new] = str(point)
# Increment the field index.
di_new += 1