def test_value_set_r1_rit(self):
"""Test of the pipe_control.value.set() function."""
# Set the current data pipe to 'mf'.
pipes.switch('relax_disp')
# Set variables.
exp_type = 'R1rho'
frq = 800.1 * 1E6
# Set an experiment type to the pipe.
set_exp_type(spectrum_id='test', exp_type=exp_type)
# Set a frequency to loop through.
spectrometer.set_frequency(id='test', frq=frq, units='Hz')
# Generate dic key.
r20_key = generate_r20_key(exp_type=exp_type, frq=frq)
# Set first similar to r2.
value.set(val=None, param='r2')
self.assertEqual(cdp.mol[0].res[0].spin[0].r2[r20_key], 10.0)
# Then set for r1.
value.set(val=None, param='r1')
print(cdp.mol[0].res[0].spin[0])
self.assertEqual(cdp.mol[0].res[0].spin[0].r1[r20_key], 2.0)
def test_value_set_r1_rit(self):
"""Test of the pipe_control.value.set() function."""
# Set the current data pipe to 'mf'.
pipes.switch('relax_disp')
# Set variables.
exp_type = 'R1rho'
frq = 800.1 * 1E6
# Set an experiment type to the pipe.
set_exp_type(spectrum_id='test', exp_type=exp_type)
# Set a frequency to loop through.
spectrometer.set_frequency(id='test', frq=frq, units='Hz')
# Generate dic key.
r20_key = generate_r20_key(exp_type=exp_type, frq=frq)
# Set first similar to r2.
value.set(val=None, param='r2')
self.assertEqual(cdp.mol[0].res[0].spin[0].r2[r20_key], 10.0)
# Then set for r1.
value.set(val=None, param='r1')
print(cdp.mol[0].res[0].spin[0])
self.assertEqual(cdp.mol[0].res[0].spin[0].r1[r20_key], 2.0)
relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)
# Relaxation dispersion CPMG constant time delay T (in s).
relax_disp.relax_time(spectrum_id=new_id, time=relax_time)
# Set the CPMG frequency.
relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id, file=file, dir=DATA_PATH, spin_id=spin_id, disp_point_col=7, data_col=10, error_col=9)
# Change the model.
relax_disp.select_model('NS MMQ 3-site linear')
# The R20 keys.
r20_1h_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=400e6)
r20_1h_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_1h_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_1h_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=1000e6)
r20_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=400e6)
r20_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=1000e6)
r20_zq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=400e6)
r20_zq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_zq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_zq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=1000e6)
r20_dq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=400e6)
r20_dq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_dq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_dq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=1000e6)
# Set the offset.
relax_disp.spin_lock_offset(spectrum_id=new_id, offset=-frequency_to_ppm(frq=offset, B0=H_frq, isotope='15N'))
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=':1', offset_col=6, data_col=10, error_col=9)
# Load the R1 data.
relax_data.read(ri_id='600MHz', ri_type='R1', frq=600e6, file='R1_600MHz.out', dir='..', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out', dir='..', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
# Change the model.
relax_disp.select_model('NS R1rho 3-site linear')
# The R20 keys.
r20_600_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=600e6)
r20_800_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)
# Manually set the parameter values.
spin = cdp.mol[0].res[0].spin[0]
spin.r2 = {
r20_600_key: 8.000284037933310,
r20_800_key: 9.000296050530716,
}
spin.pA = 0.850029879276267
spin.pB = 0.049922261890898
spin.pC = 0.100047858832835
spin.kex_AB = 500.991549690434681
spin.kex_AC = 0.0
spin.kex_BC = 2003.189830166320235
spin.dw_AB = -2.991465198310455
def loop_parameters(spins=None):
"""Generator function for looping of the parameters of the cluster.
@keyword spins: The list of spin data containers for the block.
@type spins: list of SpinContainer instances
@return: The parameter name, the parameter index (for the parameter vector), the spin index (for the cluster), and the R20 parameter key (for R20, R20A, and R20B parameters stored as dictionaries).
@rtype: str, int, int, str
"""
# Make sure that the R1 parameter is correctly set up.
r1_setup()
# The parameter index.
param_index = -1
# The R2eff model.
if cdp.model_type == 'R2eff':
# Loop over the spins.
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# Yield the two parameters.
params = ['r2eff', 'i0']
for i in range(2):
# First increment the indices.
param_index += 1
# Yield the data.
yield params[i], param_index, spin_index, None
# All other models.
else:
# First the R1 fit parameter (one per spin per field strength).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# The R1 parameter.
if 'r1' in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield 'r1', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)
# Then the R2 parameters (one per spin per field strength).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# The R2 parameter.
if 'r2' in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield 'r2', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)
# The R2A parameter.
if 'r2a' in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield 'r2a', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)
# The R2B parameter.
if 'r2b' in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield 'r2b', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)
# Then the chemical shift difference parameters 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB' (one per spin).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# Yield the data.
if 'phi_ex' in spins[spin_index].params:
param_index += 1
yield 'phi_ex', param_index, spin_index, None
if 'phi_ex_B' in spins[spin_index].params:
param_index += 1
yield 'phi_ex_B', param_index, spin_index, None
if 'phi_ex_C' in spins[spin_index].params:
param_index += 1
yield 'phi_ex_C', param_index, spin_index, None
if 'padw2' in spins[spin_index].params:
param_index += 1
yield 'padw2', param_index, spin_index, None
if 'dw' in spins[spin_index].params:
param_index += 1
yield 'dw', param_index, spin_index, None
if 'dw_AB' in spins[spin_index].params:
param_index += 1
yield 'dw_AB', param_index, spin_index, None
if 'dw_BC' in spins[spin_index].params:
param_index += 1
yield 'dw_BC', param_index, spin_index, None
if 'dw_AC' in spins[spin_index].params:
param_index += 1
yield 'dw_AC', param_index, spin_index, None
# Then a separate block for the proton chemical shift difference parameters for the MQ models (one per spin).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
if 'dwH' in spins[spin_index].params:
param_index += 1
yield 'dwH', param_index, spin_index, None
if 'dwH_AB' in spins[spin_index].params:
param_index += 1
yield 'dwH_AB', param_index, spin_index, None
if 'dwH_BC' in spins[spin_index].params:
param_index += 1
yield 'dwH_BC', param_index, spin_index, None
if 'dwH_AC' in spins[spin_index].params:
param_index += 1
yield 'dwH_AC', param_index, spin_index, None
# All other parameters (one per spin cluster).
for param in spins[0].params:
if not param in ['r1', 'r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB', 'dwH', 'dwH_AB', 'dwH_BC', 'dwH_AB']:
param_index += 1
yield param, param_index, None, None
relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)
# Relaxation dispersion CPMG constant time delay T (in s).
relax_disp.relax_time(spectrum_id=new_id, time=relax_time)
# Set the CPMG frequency.
relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)
# Change the model.
relax_disp.select_model('MMQ CR72')
# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key7 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
r20_key8 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_key9 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_key13 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6)
r20_key14 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=600e6)
r20_key15 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=800e6)
r20_key16 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)
# Relaxation dispersion CPMG constant time delay T (in s).
relax_disp.relax_time(spectrum_id=new_id, time=relax_time)
# Set the CPMG frequency.
relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)
# Change the model.
relax_disp.select_model('NS MMQ 2-site')
# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key7 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
r20_key8 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_key9 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_key13 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6)
r20_key14 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=600e6)
r20_key15 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=800e6)
r20_key16 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
pipe.switch(pipe_name=pipe_name)
print("\nModel: %s" % (model))
# Loop over the spins.
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
# Generate spin string.
spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn)
# Loop over the parameters.
print("\nOptimised parameters for spin: %s" % (spin_string))
for param in cur_spin.params + ['chi2']:
# Get the value.
if param in ['r1', 'r2']:
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
# Generate the R20 key.
r20_key = generate_r20_key(exp_type=exp_type, frq=frq)
# Get the value.
value = getattr(cur_spin, param)[r20_key]
# Print value.
print("%-10s %-6s %-6s %3.8f" % ("Parameter:", param, "Value:", value))
# For all other parameters.
else:
# Get the value.
value = getattr(cur_spin, param)
# Print value.
print("%-10s %-6s %-6s %3.8f" % ("Parameter:", param, "Value:", value))
# NS : r2a = r2b
model_analyse_list.append(MODEL_NS_CPMG_2SITE_3D)
model_analyse_list.append(MODEL_NS_CPMG_2SITE_STAR)
model_analyse_list.append(MODEL_NS_CPMG_2SITE_EXPANDED)
# NS full : r2a = r2b
model_analyse_list.append(MODEL_NS_CPMG_2SITE_3D_FULL)
model_analyse_list.append(MODEL_NS_CPMG_2SITE_STAR_FULL)
# The model.
model_analyse = model_analyse_list[10]
## Experiments
# Exp 1
sfrq_1 = 500.0*1E6
r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1)
time_T2_1 = 0.05
ncycs_1 = [2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 40, 50]
# Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence.
#r2eff_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05]
r2eff_errs_1 = [0.0] * len(ncycs_1)
exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_1]
sfrq_2 = 600.0*1E6
r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2)
time_T2_2 = 0.06
ncycs_2 = [2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 40, 60]
# Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence.
#r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05]
r2eff_errs_2 = [0.0] * len(ncycs_2)
exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2]
def loop_parameters(spins=None):
"""Generator function for looping of the parameters of the cluster.
@keyword spins: The list of spin data containers for the block.
@type spins: list of SpinContainer instances
@return: The parameter name, the parameter index (for the parameter vector), the spin index (for the cluster), and the R20 parameter key (for R20, R20A, and R20B parameters stored as dictionaries).
@rtype: str, int, int, str
"""
# Make sure that the R1 parameter is correctly set up.
r1_setup()
# The parameter index.
param_index = -1
# The R2eff model.
if cdp.model_type == 'R2eff':
# Loop over the spins.
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# Yield the two parameters.
params = ['r2eff', 'i0']
for i in range(2):
# First increment the indices.
param_index += 1
# Yield the data.
yield params[i], param_index, spin_index, None
# All other models.
else:
# First the R1 fit parameter (one per spin per field strength).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# The R1 parameter.
if 'r1' in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield 'r1', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)
# Then the R2 parameters (one per spin per field strength).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# The R2 parameter.
if 'r2' in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield 'r2', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)
# The R2A parameter.
if 'r2a' in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield 'r2a', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)
# The R2B parameter.
if 'r2b' in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield 'r2b', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)
# Then the chemical shift difference parameters 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB' (one per spin).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# Yield the data.
if 'phi_ex' in spins[spin_index].params:
param_index += 1
yield 'phi_ex', param_index, spin_index, None
if 'phi_ex_B' in spins[spin_index].params:
param_index += 1
yield 'phi_ex_B', param_index, spin_index, None
if 'phi_ex_C' in spins[spin_index].params:
param_index += 1
yield 'phi_ex_C', param_index, spin_index, None
if 'padw2' in spins[spin_index].params:
param_index += 1
yield 'padw2', param_index, spin_index, None
if 'dw' in spins[spin_index].params:
param_index += 1
yield 'dw', param_index, spin_index, None
if 'dw_AB' in spins[spin_index].params:
param_index += 1
yield 'dw_AB', param_index, spin_index, None
if 'dw_BC' in spins[spin_index].params:
param_index += 1
yield 'dw_BC', param_index, spin_index, None
if 'dw_AC' in spins[spin_index].params:
param_index += 1
yield 'dw_AC', param_index, spin_index, None
# Then a separate block for the proton chemical shift difference parameters for the MQ models (one per spin).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
if 'dwH' in spins[spin_index].params:
param_index += 1
yield 'dwH', param_index, spin_index, None
if 'dwH_AB' in spins[spin_index].params:
param_index += 1
yield 'dwH_AB', param_index, spin_index, None
if 'dwH_BC' in spins[spin_index].params:
param_index += 1
yield 'dwH_BC', param_index, spin_index, None
if 'dwH_AC' in spins[spin_index].params:
param_index += 1
yield 'dwH_AC', param_index, spin_index, None
# All other parameters (one per spin cluster).
for param in spins[0].params:
if not param in ['r1', 'r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB', 'dwH', 'dwH_AB', 'dwH_BC', 'dwH_AB']:
param_index += 1
yield param, param_index, None, None
# NS : r2a = r2b
model_analyse_list.append(MODEL_NS_CPMG_2SITE_3D)
model_analyse_list.append(MODEL_NS_CPMG_2SITE_STAR)
model_analyse_list.append(MODEL_NS_CPMG_2SITE_EXPANDED)
# NS full : r2a = r2b
model_analyse_list.append(MODEL_NS_CPMG_2SITE_3D_FULL)
model_analyse_list.append(MODEL_NS_CPMG_2SITE_STAR_FULL)
# The model.
model_analyse = model_analyse_list[0]
## Experiments
# Exp 1
sfrq_1 = 599.8908617*1E6
r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1)
time_T2_1 = 0.06
ncycs_1 = [28, 4, 32, 60, 2, 10, 16, 8, 20, 50, 18, 40, 6, 12, 24]
# Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence.
#r2eff_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05]
r2eff_errs_1 = [0.0] * len(ncycs_1)
exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_1]
sfrq_2 = 499.8908617*1E6
r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2)
time_T2_2 = 0.04
ncycs_2 = [20, 16, 10, 36, 2, 12, 4, 22, 18, 40, 14, 26, 8, 32, 24, 6, 28 ]
# Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence.
#r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05]
r2eff_errs_2 = [0.0] * len(ncycs_2)
exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2]
def loop_parameters(spins=None):
"""Generator function for looping of the model parameters of the cluster.
@keyword spins: The list of spin data containers for the block.
@type spins: list of SpinContainer instances
@return: The parameter name, the parameter index (for the parameter vector), the spin index (for the cluster), and the R20 parameter key (for R20, R20A, and R20B parameters stored as dictionaries).
@rtype: str, int, int, str
"""
# Make sure that the R1 parameter is correctly set up.
r1_setup()
# The parameter index.
param_index = -1
# The R2eff model.
if cdp.model_type == 'R2eff':
# Loop over the spins.
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# One or two parameters.
params = ['r2eff']
if has_exponential_exp_type():
params = ['r2eff', 'i0']
# Yield the parameters.
for param in params:
# First increment the indices.
param_index += 1
# Yield the data.
yield param, param_index, spin_index, None
# All other models.
else:
# First the R1 fit parameter (one per spin per field strength).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# The parameters.
for param in PARAMS_R1:
if param in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield param, param_index, spin_index, generate_r20_key(
exp_type=exp_type, frq=frq)
# Then the R2 parameters (one per spin per field strength).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# The parameters.
for param in PARAMS_R20:
if param in spins[spin_index].params:
for exp_type, frq in loop_exp_frq():
param_index += 1
yield param, param_index, spin_index, generate_r20_key(
exp_type=exp_type, frq=frq)
# Then the chemical shift difference parameters (one per spin).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# Yield the data.
for param in PARAMS_CHEM_SHIFT_DIFF:
if param in spins[spin_index].params:
param_index += 1
yield param, param_index, spin_index, None
# Then a separate block for the proton chemical shift difference parameters for the MQ models (one per spin).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# Yield the data.
for param in PARAMS_CHEM_SHIFT_DIFF_MMQ:
if param in spins[spin_index].params:
param_index += 1
yield param, param_index, spin_index, None
# All other parameters (one per spin cluster).
for spin_index in range(len(spins)):
# Skip deselected spins.
if not spins[spin_index].select:
continue
# The parameters.
for param in spins[0].params:
if not param in PARAMS_SPIN:
param_index += 1
yield param, param_index, None, None
# No more spins.
break
relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id,
file=file,
dir='..',
spin_id=spin_id,
disp_point_col=1,
data_col=2,
error_col=3)
# Change the model.
relax_disp.select_model('NS MMQ 2-site')
# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
# Manually set the parameter values.
spin_N = cdp.mol[0].res[0].spin[1]
spin_N.r2 = {
r20_key1: 8.412998,
r20_key2: 8.847946,
r20_key3: 10.329567,
r20_key4: 6.779626,
r20_key5: 7.089813,
r20_key6: 5.610770
def test_tp02_data_to_tp02(self):
"""Test the GUI analysis with the relaxation dispersion 'TP02' model fitting to the 'TP02' synthetic data."""
# The paths to the data files.
data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'dispersion' + sep + 'r1rho_off_res_tp02' + sep
# Simulate the new analysis wizard, selecting the fixed time CPMG experiment.
analysis = self.new_analysis_wizard(analysis_type='disp')
# Change the results directory.
analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir))
# Create the sequence data.
self._execute_uf(uf_name='spin.create',
res_name='Trp',
res_num=1,
spin_name='N')
interpreter.flush()
self._execute_uf(uf_name='spin.create',
res_name='Trp',
res_num=2,
spin_name='N')
interpreter.flush()
self._execute_uf(uf_name='sequence.display')
interpreter.flush()
# Set up the nuclear isotopes.
analysis.spin_isotope()
uf_store['spin.isotope'].page.SetValue('spin_id', '')
uf_store['spin.isotope'].wizard._go_next()
interpreter.flush() # Required because of the asynchronous uf call.
# Load the chemical shift data.
self._execute_uf(uf_name='chemical_shift.read',
file='ref_500MHz.list',
dir=data_path)
interpreter.flush()
# The spectral data.
frq = [500, 800]
frq_label = ['500MHz', '800MHz']
error = 200000.0
data = []
spin_lock = [
None, 1000.0, 1500.0, 2000.0, 2500.0, 3000.0, 3500.0, 4000.0,
4500.0, 5000.0, 5500.0, 6000.0
]
for frq_index in range(len(frq)):
for spin_lock_index in range(len(spin_lock)):
# The reference.
if spin_lock[spin_lock_index] == None:
id = 'ref_%s' % frq_label[frq_index]
file = "ref_%s.list" % frq_label[frq_index]
# Normal data.
else:
id = "nu_%s_%s" % (spin_lock[spin_lock_index],
frq_label[frq_index])
file = "nu_%s_%s.list" % (spin_lock[spin_lock_index],
frq_label[frq_index])
# Append the data.
data.append(
[id, file, spin_lock[spin_lock_index], frq[frq_index]])
# Load the R1 data.
for frq_index in range(len(frq)):
label = 'R1_%s' % frq_label[frq_index]
self._execute_uf(uf_name='relax_data.read',
ri_id=label,
ri_type='R1',
frq=frq[frq_index] * 1e6,
file='%s.out' % label,
dir=data_path,
mol_name_col=1,
res_num_col=2,
res_name_col=3,
spin_num_col=4,
spin_name_col=5,
data_col=6,
error_col=7)
interpreter.flush()
# Set up the peak intensity wizard.
analysis.peak_wizard_launch(None)
wizard = analysis.peak_wizard
# The spectra.
for id, file, field, H_frq in data:
wizard.setup_page(page='read',
file=data_path + file,
spectrum_id=id,
int_method='height',
dim=1)
wizard._apply(None)
wizard._skip(None)
# The error type.
page = wizard.get_page(wizard.page_indices['err_type'])
page.selection = 'rmsd'
wizard._go_next(None)
# Baseplane RMSD.
for id, file, field, H_frq in data:
wizard.setup_page(page='rmsd', spectrum_id=id, error=error)
wizard._apply(None)
wizard._skip(None)
# The experiment type.
for id, file, field, H_frq in data:
wizard.setup_page(page='exp_type',
spectrum_id=id,
exp_type='R1rho')
wizard._apply(None)
wizard._skip(None)
# Set the spectrometer frequency.
for id, file, field, H_frq in data:
wizard.setup_page(page='spectrometer_frequency',
id=id,
frq=H_frq,
units='MHz')
wizard._apply(None)
wizard._skip(None)
# Set the relaxation times.
for id, file, field, H_frq in data:
wizard.setup_page(page='relax_time', spectrum_id=id, time=0.1)
wizard._apply(None)
wizard._skip(None)
# Set the relaxation dispersion spin-lock field strength (nu1).
for id, file, field, H_frq in data:
wizard.setup_page(page='spin_lock_field',
spectrum_id=id,
field=field)
wizard._apply(None)
wizard._skip(None)
# Set the spin-lock offset.
for id, file, field, H_frq in data:
wizard.setup_page(page='spin_lock_offset',
spectrum_id=id,
offset=110.0)
wizard._apply(None)
wizard._skip(None)
# Flush all wx events (to allow the spectrum list GUI element to populate all its rows).
wx.Yield()
# Simulate right clicking in the spectrum list element to test the popup menu.
analysis.peak_intensity.on_right_click(Fake_right_click())
# Simulate the popup menu entries to catch bugs there (just apply the user functions with the currently set values).
# FIXME: skipping the checks for certain wxPython bugs.
if status.relax_mode != 'gui' and wx.version(
) != '2.9.4.1 gtk2 (classic)':
analysis.peak_intensity.action_relax_disp_spin_lock_field(item=4)
uf_store['relax_disp.spin_lock_field'].wizard._go_next()
interpreter.flush()
analysis.peak_intensity.action_relax_disp_exp_type(item=5)
uf_store['relax_disp.exp_type'].wizard._go_next()
interpreter.flush()
analysis.peak_intensity.action_relax_disp_relax_time(item=0)
uf_store['relax_disp.relax_time'].wizard._go_next()
interpreter.flush()
analysis.peak_intensity.action_spectrometer_frq(item=10)
uf_store['spectrometer.frequency'].wizard._go_next()
interpreter.flush()
# Deselect all but the 'TP02' model.
models = [MODEL_R2EFF, MODEL_NOREX, MODEL_TP02]
for i in range(len(analysis.model_field.models_stripped)):
if analysis.model_field.models_stripped[i] in models:
analysis.model_field.select[i] = True
else:
analysis.model_field.select[i] = False
analysis.model_field.modify()
# Set the grid search size and number of MC sims.
analysis.grid_inc.SetValue(4)
analysis.mc_sim_num.SetValue(3)
# Optimisation speedups.
analysis.opt_func_tol = 1e-10
analysis.opt_max_iterations = 10000
# Execute relax.
analysis.execute(
wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED,
analysis.button_exec_relax.GetId()))
# Wait for execution to complete.
analysis.thread.join()
# Flush all wx events.
wx.Yield()
# Exceptions in the thread.
self.check_exceptions()
# Check the relax controller.
# FIXME: skipping the checks for certain wxPython bugs.
if status.relax_mode != 'gui' and wx.version(
) != '2.9.4.1 gtk2 (classic)':
self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(),
100)
self.assertEqual(self.app.gui.controller.main_gauge.GetValue(),
100)
# The original parameters.
r1rho_prime = [[10.0, 15.0], [12.0, 18.0]]
pA = 0.7654321
kex = 1234.56789
delta_omega = [7.0, 9.0]
# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)
# Switch to the 'TP02' model data pipe, then check for each spin.
switch("%s - %s" % ('TP02', get_bundle()))
spin_index = 0
for spin, spin_id in spin_loop(return_id=True):
# Printout.
print("\nSpin %s." % spin_id)
# Check the fitted parameters.
self.assertAlmostEqual(spin.r2[r20_key1] / 10,
r1rho_prime[spin_index][0] / 10, 4)
self.assertAlmostEqual(spin.r2[r20_key2] / 10,
r1rho_prime[spin_index][1] / 10, 4)
self.assertAlmostEqual(spin.dw, delta_omega[spin_index], 3)
self.assertAlmostEqual(spin.kex / 1000.0, kex / 1000.0, 3)
# Increment the spin index.
spin_index += 1
def test_tp02_data_to_tp02(self):
"""Test the GUI analysis with the relaxation dispersion 'TP02' model fitting to the 'TP02' synthetic data."""
# The paths to the data files.
data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_off_res_tp02'+sep
# Simulate the new analysis wizard, selecting the fixed time CPMG experiment.
analysis = self.new_analysis_wizard(analysis_type='disp')
# Change the results directory.
analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir))
# Create the sequence data.
self._execute_uf(uf_name='spin.create', res_name='Trp', res_num=1, spin_name='N')
interpreter.flush()
self._execute_uf(uf_name='spin.create', res_name='Trp', res_num=2, spin_name='N')
interpreter.flush()
self._execute_uf(uf_name='sequence.display')
interpreter.flush()
# Set up the nuclear isotopes.
analysis.spin_isotope()
uf_store['spin.isotope'].page.SetValue('spin_id', '')
uf_store['spin.isotope'].wizard._go_next()
interpreter.flush() # Required because of the asynchronous uf call.
# Load the chemical shift data.
self._execute_uf(uf_name='chemical_shift.read', file='ref_500MHz.list', dir=data_path)
interpreter.flush()
# The spectral data.
frq = [500, 800]
frq_label = ['500MHz', '800MHz']
error = 200000.0
data = []
spin_lock = [None, 1000.0, 1500.0, 2000.0, 2500.0, 3000.0, 3500.0, 4000.0, 4500.0, 5000.0, 5500.0, 6000.0]
for frq_index in range(len(frq)):
for spin_lock_index in range(len(spin_lock)):
# The reference.
if spin_lock[spin_lock_index] == None:
id = 'ref_%s' % frq_label[frq_index]
file = "ref_%s.list" % frq_label[frq_index]
# Normal data.
else:
id = "nu_%s_%s" % (spin_lock[spin_lock_index], frq_label[frq_index])
file = "nu_%s_%s.list" % (spin_lock[spin_lock_index], frq_label[frq_index])
# Append the data.
data.append([id, file, spin_lock[spin_lock_index], frq[frq_index]])
# Load the R1 data.
for frq_index in range(len(frq)):
label = 'R1_%s' % frq_label[frq_index]
self._execute_uf(uf_name='relax_data.read', ri_id=label, ri_type='R1', frq=frq[frq_index]*1e6, file='%s.out'%label, dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
interpreter.flush()
# Set up the peak intensity wizard.
analysis.peak_wizard_launch(None)
wizard = analysis.peak_wizard
# The spectra.
for id, file, field, H_frq in data:
wizard.setup_page(page='read', file=data_path+file, spectrum_id=id, int_method='height', dim=1)
wizard._apply(None)
wizard._skip(None)
# The error type.
page = wizard.get_page(wizard.page_indices['err_type'])
page.selection = 'rmsd'
wizard._go_next(None)
# Baseplane RMSD.
for id, file, field, H_frq in data:
wizard.setup_page(page='rmsd', spectrum_id=id, error=error)
wizard._apply(None)
wizard._skip(None)
# The experiment type.
for id, file, field, H_frq in data:
wizard.setup_page(page='exp_type', spectrum_id=id, exp_type='R1rho')
wizard._apply(None)
wizard._skip(None)
# Set the spectrometer frequency.
for id, file, field, H_frq in data:
wizard.setup_page(page='spectrometer_frequency', id=id, frq=H_frq, units='MHz')
wizard._apply(None)
wizard._skip(None)
# Set the relaxation times.
for id, file, field, H_frq in data:
wizard.setup_page(page='relax_time', spectrum_id=id, time=0.1)
wizard._apply(None)
wizard._skip(None)
# Set the relaxation dispersion spin-lock field strength (nu1).
for id, file, field, H_frq in data:
wizard.setup_page(page='spin_lock_field', spectrum_id=id, field=field)
wizard._apply(None)
wizard._skip(None)
# Set the spin-lock offset.
for id, file, field, H_frq in data:
wizard.setup_page(page='spin_lock_offset', spectrum_id=id, offset=110.0)
wizard._apply(None)
wizard._skip(None)
# Flush all wx events (to allow the spectrum list GUI element to populate all its rows).
wx.Yield()
# Simulate right clicking in the spectrum list element to test the popup menu.
analysis.peak_intensity.on_right_click(Fake_right_click())
# Simulate the popup menu entries to catch bugs there (just apply the user functions with the currently set values).
# FIXME: skipping the checks for certain wxPython bugs.
if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2 (classic)':
analysis.peak_intensity.action_relax_disp_spin_lock_field(item=4)
uf_store['relax_disp.spin_lock_field'].wizard._go_next()
interpreter.flush()
analysis.peak_intensity.action_relax_disp_exp_type(item=5)
uf_store['relax_disp.exp_type'].wizard._go_next()
interpreter.flush()
analysis.peak_intensity.action_relax_disp_relax_time(item=0)
uf_store['relax_disp.relax_time'].wizard._go_next()
interpreter.flush()
analysis.peak_intensity.action_spectrometer_frq(item=10)
uf_store['spectrometer.frequency'].wizard._go_next()
interpreter.flush()
# Deselect all but the 'TP02' model.
models = [MODEL_R2EFF, MODEL_NOREX, MODEL_TP02]
for i in range(len(analysis.model_field.models_stripped)):
if analysis.model_field.models_stripped[i] in models:
analysis.model_field.select[i] = True
else:
analysis.model_field.select[i] = False
analysis.model_field.modify()
# Set the grid search size and number of MC sims.
analysis.grid_inc.SetValue(4)
analysis.mc_sim_num.SetValue(3)
# Optimisation speedups.
analysis.opt_func_tol = 1e-10
analysis.opt_max_iterations = 10000
# Execute relax.
analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId()))
# Wait for execution to complete.
analysis.thread.join()
# Flush all wx events.
wx.Yield()
# Exceptions in the thread.
self.check_exceptions()
# Check the relax controller.
# FIXME: skipping the checks for certain wxPython bugs.
if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2 (classic)':
self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(), 100)
self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100)
# The original parameters.
r1rho_prime = [[10.0, 15.0], [12.0, 18.0]]
pA = 0.7654321
kex = 1234.56789
delta_omega = [7.0, 9.0]
# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)
# Switch to the 'TP02' model data pipe, then check for each spin.
switch("%s - %s" % ('TP02', get_bundle()))
spin_index = 0
for spin, spin_id in spin_loop(return_id=True):
# Printout.
print("\nSpin %s." % spin_id)
# Check the fitted parameters.
self.assertAlmostEqual(spin.r2[r20_key1]/10, r1rho_prime[spin_index][0]/10, 4)
self.assertAlmostEqual(spin.r2[r20_key2]/10, r1rho_prime[spin_index][1]/10, 4)
self.assertAlmostEqual(spin.dw, delta_omega[spin_index], 3)
self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 3)
# Increment the spin index.
spin_index += 1
relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id,
file=file,
dir=DATA_PATH,
spin_id=spin_id,
disp_point_col=7,
data_col=10,
error_col=9)
# Change the model.
relax_disp.select_model('NS MMQ 3-site linear')
# The R20 keys.
r20_1h_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=400e6)
r20_1h_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=600e6)
r20_1h_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=800e6)
r20_1h_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=1000e6)
r20_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=400e6)
r20_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=1000e6)
r20_zq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=400e6)
r20_zq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_zq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_zq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=1000e6)
r20_dq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=400e6)
relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)
# Relaxation dispersion CPMG constant time delay T (in s).
relax_disp.relax_time(spectrum_id=new_id, time=relax_time)
# Set the CPMG frequency.
relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id, file=file, dir='../..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)
# Change the model.
relax_disp.select_model('NS MMQ 2-site')
# The R20 keys.
r20_key_sq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key_sq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key_sq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key_1h_sq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key_1h_sq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key_1h_sq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_key_zq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
r20_key_zq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_key_zq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_key_dq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
r20_key_dq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_key_dq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_key_mq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
r20_key_mq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6)
r20_key_mq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6)
r20_key_1h_mq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6)
frq=800e6,
file='R1_800MHz.out',
dir='..',
mol_name_col=1,
res_num_col=2,
res_name_col=3,
spin_num_col=4,
spin_name_col=5,
data_col=6,
error_col=7)
# Change the model.
relax_disp.select_model('TP02')
# The R20 keys.
r20_600_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=600e6)
r20_800_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)
# Manually set the parameter values.
spin_N = cdp.mol[0].res[0].spin[0]
spin_N.r2 = {
r20_600_key: 9.108060397660111,
r20_800_key: 13.793213528551924,
}
spin_N.pA = 0.945912353996981
spin_N.pB = 0.054087646003019
spin_N.kex = 367.981715073974556
spin_N.dw = 4.305697497613982
spin_N.ri_data['600MHz'] = 3.179051390898238
spin_N.ri_data['800MHz'] = 4.452840879991469
return_id=True,
skip_desel=True):
# Generate spin string.
spin_string = generate_spin_string(spin=cur_spin,
mol_name=mol_name,
res_num=resi,
res_name=resn)
# Loop over the parameters.
print("\nOptimised parameters for spin: %s" % (spin_string))
for param in cur_spin.params + ['chi2']:
# Get the value.
if param in ['r1', 'r2']:
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
# Generate the R20 key.
r20_key = generate_r20_key(exp_type=exp_type, frq=frq)
# Get the value.
value = getattr(cur_spin, param)[r20_key]
# Print value.
print("%-10s %-6s %-6s %3.8f" %
("Parameter:", param, "Value:", value))
# For all other parameters.
else:
# Get the value.
value = getattr(cur_spin, param)
# Print value.
print("%-10s %-6s %-6s %3.8f" %
relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)
# Relaxation dispersion CPMG constant time delay T (in s).
relax_disp.relax_time(spectrum_id=new_id, time=relax_time)
# Set the CPMG frequency.
relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id, file=file, dir='../..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)
# Change the model.
relax_disp.select_model('NS MMQ 2-site')
# The R20 keys.
r20_key_sq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key_sq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key_sq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key_1h_sq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key_1h_sq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key_1h_sq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_key_zq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
r20_key_zq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_key_zq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_key_dq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
r20_key_dq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_key_dq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_key_mq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
r20_key_mq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6)
r20_key_mq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6)
r20_key_1h_mq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6)
relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)
# Relaxation dispersion CPMG constant time delay T (in s).
relax_disp.relax_time(spectrum_id=new_id, time=relax_time)
# Set the CPMG frequency.
relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)
# Read the R2eff data.
relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)
# Change the model.
relax_disp.select_model('NS MMQ 2-site')
# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
# Manually set the parameter values.
spin_N = cdp.mol[0].res[0].spin[1]
spin_N.r2 = {r20_key1: 8.412998, r20_key2: 8.847946, r20_key3: 10.329567, r20_key4: 6.779626, r20_key5: 7.089813, r20_key6: 5.610770}
spin_N.pA = 0.947960
spin_N.kex = 408.394
spin_N.dw = 4.369907
spin_N.dwH = -0.267240
# Optimisation.