def run_analysis(self):
"""Execute the calculation."""
# Optimisation precision.
Relax_disp.opt_func_tol = self.data.opt_func_tol
Relax_disp.opt_max_iterations = self.data.opt_max_iterations
# Execute.
Relax_disp(pipe_name=self.data.pipe_name, pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, models=self.data.models, grid_inc=self.data.inc, mc_sim_num=self.data.mc_sim_num, exp_mc_sim_num=self.data.exp_mc_sim_num, pre_run_dir=self.data.pre_run_dir, mc_sim_all_models=self.data.mc_sim_all_models, insignificance=self.data.insignificance, numeric_only=self.data.numeric_only, r1_fit=self.data.r1_fit)
# Alias the relax data store data.
data = ds.relax_gui.analyses[self.data_index]
# Create the data pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
# The path to the data files.
data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'dispersion' + sep + 'Hansen'
# Load the saved base pipe containing R2eff data.
results.read(data_path + sep + 'r2eff_pipe')
deselect.spin(":4")
# Set the nuclear isotope data.
spin.isotope('15N')
# Auto-analysis execution.
##########################
# Run fast.
Relax_disp.opt_func_tol = 1e-5
Relax_disp.opt_max_iterations = 10000
# Do not change!
Relax_disp(pipe_name=pipe_name,
pipe_bundle=pipe_bundle,
results_dir=ds.tmpdir,
models=MODELS,
grid_inc=GRID_INC,
mc_sim_num=MC_NUM,
numeric_only=ds.numeric_only)
# Set the spin-lock offset.
relax_disp.spin_lock_offset(spectrum_id=id, offset=offset)
# Set the relaxation times (in s).
relax_disp.relax_time(spectrum_id=id, time=relax_time)
# Set the NMR field strength of the spectrum.
spectrometer.frequency(id=id, frq=H_frq)
# Load the R1 data.
relax_data.read(ri_id='900MHz', ri_type='R1', frq=900.21422558574e6, file='R1_relax.out', 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)
# Clustering (only to be activated after an initial analysis without clustering).
#relax_disp.cluster(cluster_id='cluster', spin_id=':1-50')
# Read the chemical shift data.
chemical_shift.read(file='chemical_shifts.list', dir=DATA_PATH)
# Deselect unresolved spins.
deselect.read(file='unresolved', dir=DATA_PATH, res_num_col=1)
# Auto-analysis execution.
##########################
# Do not change!
Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL, insignificance=INSIGNIFICANCE, numeric_only=NUMERIC_ONLY)
#Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL, pre_run_dir=PRE_RUN_DIR, insignificance=INSIGNIFICANCE, numeric_only=NUMERIC_ONLY, mc_sim_all_models=MC_SIM_ALL_MODELS)
# To speed up the analysis, only select a few spins.
deselect.all()
# Load the experiments settings file.
residues = open(ds.data_path + sep + 'global_fit_residues.txt', 'r')
residueslines = residues.readlines()
residues.close()
# Split the line string into number and text.
r = re.compile("([a-zA-Z]+)([0-9]+)([a-zA-Z]+)(-)([a-zA-Z]+)")
for i, line in enumerate(residueslines):
if line[0] == "#":
continue
else:
re_split = r.match(line)
#print re_split.groups()
resn = re_split.group(1)
resi = int(re_split.group(2))
isotope = re_split.group(3)
select.spin(spin_id=':%i@%s' % (resi, isotope), change_all=False)
# Run the analysis.
Relax_disp(pipe_name=ds.pipe_name,
pipe_bundle=ds.pipe_bundle,
results_dir=ds.results_dir,
models=ds.models,
grid_inc=ds.grid_inc,
exp_mc_sim_num=ds.exp_mc_sim_num)
# Load the initial state setup
state.load(state='ini_setup.bz2')
# Set settings for run.
results_directory = 'temp'
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
MODELS = ['R2eff']
GRID_INC = 5
MC_NUM = 3
MODSEL = 'AIC'
# Execute
Relax_disp(pipe_name=pipe_name,
pipe_bundle=pipe_bundle,
results_dir=results_directory,
models=MODELS,
grid_inc=GRID_INC,
mc_sim_num=MC_NUM,
modsel=MODSEL)
# Delete the "base pipe"
pipe.delete(pipe_name='base pipe')
# Save the program state.
state.save('r2eff_pipe', force=True)
# Delete data result directory
shutil.rmtree(results_directory)
])
spectrum.error_analysis(subset=[
'800_reference.in', '800_66.667.in', '800_133.33.in', '800_133.33.in.bis',
'800_200.in', '800_266.67.in', '800_333.33.in', '800_400.in',
'800_466.67.in', '800_533.33.in', '800_533.33.in.bis', '800_600.in',
'800_666.67.in', '800_733.33.in', '800_800.in', '800_866.67.in',
'800_933.33.in', '800_933.33.in.bis', '800_1000.in'
])
# Deselect unresolved spins.
deselect.read(file='unresolved',
dir=data_path + sep + '500_MHz',
res_num_col=1)
deselect.read(file='unresolved',
dir=data_path + sep + '800_MHz',
res_num_col=1)
# Spin subset.
select.spin(':63-70', change_all=True)
# Auto-analysis execution.
##########################
# Do not change!
Relax_disp(pipe_name=pipe_name,
pipe_bundle=pipe_bundle,
results_dir=RESULTS_DIR,
models=MODELS,
grid_inc=GRID_INC,
mc_sim_num=MC_NUM)
res_num_col=1)
deselect.read(file='unresolved',
dir=data_path + sep + '800_MHz',
res_num_col=1)
# Select just spins :70@N and :71@N.
select.spin(":70-71", change_all=True)
# Auto-analysis execution (manually replicated).
################################################
# Do not change!
if False:
Relax_disp(pipe_name=pipe_name,
pipe_bundle=pipe_bundle,
models=MODELS,
grid_inc=GRID_INC,
mc_sim_num=MC_NUM)
# The 'R2eff' model.
#~~~~~~~~~~~~~~~~~~~
# Pipe setup.
model = MODELS[0]
pipe.copy(pipe_from='base pipe', pipe_to=model, bundle_to='relax_disp')
pipe.switch(pipe_name=model)
relax_disp.select_model(model='R2eff')
# Optimisation.
calc(verbosity=1)
# Set the NMR field strength of the spectrum.
spectrometer.frequency(id=id, frq=H_frq * 1e6)
# Relaxation dispersion CPMG constant time delay T (in s).
relax_disp.relax_time(spectrum_id=id, time=delay)
# set each spectrum noise RMSD
if ndat == 1:
spectrum.baseplane_rmsd(error=24000, spectrum_id=id, spin_id=None)
elif ndat == 6:
spectrum.baseplane_rmsd(error=65000, spectrum_id=id, spin_id=None)
# Peak intensity error analysis.
spectrum.error_analysis_per_field()
# Auto-analysis execution.
##########################
# Do not change!
Relax_disp(pipe_name=pipe_name,
pipe_bundle=pipe_bundle,
results_dir=ds.tmpdir,
models=MODELS,
grid_inc=GRID_INC,
mc_sim_num=MC_NUM,
modsel=MODSEL,
pre_run_dir=PRE_RUN_DIR,
insignificance=INSIGNIFICANCE,
numeric_only=NUMERIC_ONLY,
mc_sim_all_models=MC_SIM_ALL_MODELS)
for key in cdp.clustering:
print(key, cdp.clustering[key])
# Print parameter kex before copying.
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True,
return_id=True,
skip_desel=True):
print(cur_spin.kex)
## Make advanced parameter copy.
# It is more advanced than the value.copy user function, in that clustering is taken into account.
# When the destination data pipe has spin clusters defined, then the new parameter values, when required, will be taken as the median value.
relax_disp.parameter_copy(pipe_from=ini_pipe_name, pipe_to=ds.pipe_name)
# Print parameter kex after copying.
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True,
return_id=True,
skip_desel=True):
print(cur_spin.kex)
pipe.display()
# Run the analysis.
Relax_disp(pipe_name=ds.pipe_name,
pipe_bundle=ds.pipe_bundle_cluster,
results_dir=ds.results_dir,
models=ds.models,
grid_inc=ds.grid_inc,
mc_sim_num=ds.mc_sim_num,
modsel=ds.modsel)
# Specify the duplicated spectra.
spectrum.replicated(spectrum_ids=['600_ncyc1', '600_ncyc1b'])
spectrum.replicated(spectrum_ids=['600_ncyc2', '600_ncyc2b'])
spectrum.replicated(spectrum_ids=['600_ncyc3', '600_ncyc3b'])
spectrum.replicated(spectrum_ids=['800_ncyc1', '800_ncyc1b'])
spectrum.replicated(spectrum_ids=['800_ncyc2', '800_ncyc2b'])
spectrum.replicated(spectrum_ids=['800_ncyc3', '800_ncyc3b'])
# Measured chemical shift differences.
value.set(val=0.625, param='dw', spin_id=":135")
value.set(val=0.033, param='dwH', spin_id=":135")
value.set(val=0.981, param='dw', spin_id=":137")
value.set(val=0.010, param='dwH', spin_id=":137")
#value.set(val=0.5, param='pA')
#value.set(val=67.5, param='kex')
# Cluster all spins.
relax_disp.cluster(cluster_id='all', spin_id=":135-137")
# Auto-analysis execution.
##########################
# Do not change!
Relax_disp(pipe_name=pipe_name,
pipe_bundle=pipe_bundle,
results_dir=RESULTS_DIR,
pre_run_dir='mq_cr72_analysis',
models=MODELS,
grid_inc=GRID_INC,
mc_sim_num=MC_NUM)
relax_disp.relax_time(spectrum_id=id, time=0.1)
# Errors.
spectrum.baseplane_rmsd(error=1000000.0, spectrum_id=id)
# Peak intensity error analysis.
spectrum.error_analysis(subset=[
'500_reference', '500_66.6666', '500_133.3333', '500_200.0',
'500_266.6666', '500_333.3333', '500_400.0', '500_466.6666',
'500_533.3333', '500_600.0', '500_666.6666', '500_733.3333', '500_800.0',
'500_866.6666', '500_933.3333', '500_1000.0'
])
spectrum.error_analysis(subset=[
'800_reference', '800_66.6666', '800_133.3333', '800_200.0',
'800_266.6666', '800_333.3333', '800_400.0', '800_466.6666',
'800_533.3333', '800_600.0', '800_666.6666', '800_733.3333', '800_800.0',
'800_866.6666', '800_933.3333', '800_1000.0'
])
# Auto-analysis execution.
##########################
# Do not change!
Relax_disp(pipe_name=pipe_name,
pipe_bundle=pipe_bundle,
results_dir=RESULTS_DIR,
models=MODELS)
# Save the program state.
state.save('r2eff_values', force=True)
relax_disp.relax_time(spectrum_id=id, time=0.015) # Specify the duplicated spectra. spectrum.replicated(spectrum_ids=['600_ncyc1', '600_ncyc1b']) spectrum.replicated(spectrum_ids=['600_ncyc2', '600_ncyc2b']) spectrum.replicated(spectrum_ids=['600_ncyc3', '600_ncyc3b']) spectrum.replicated(spectrum_ids=['800_ncyc1', '800_ncyc1b']) spectrum.replicated(spectrum_ids=['800_ncyc2', '800_ncyc2b']) spectrum.replicated(spectrum_ids=['800_ncyc3', '800_ncyc3b']) # Measured chemical shift differences. value.set(val=0.625, param='dw', spin_id=":135") value.set(val=0.033, param='dwH', spin_id=":135") value.set(val=0.981, param='dw', spin_id=":137") value.set(val=0.010, param='dwH', spin_id=":137") # Optimised parameters from the paper. value.set(val=0.5, param='pA') value.set(val=67.5, param='kex') # Auto-analysis execution. ########################## # Run faster. Relax_disp.opt_func_tol = 1e-10 Relax_disp.opt_max_iterations = 10000 # Do not change! Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, results_dir=ds.tmpdir, models=ds.models, grid_inc=GRID_INC, mc_sim_num=MC_NUM)
# Set the relaxation times.
relax_disp.relax_time(spectrum_id=data[i][0], time=data[i][3])
# Set the spectrometer frequency.
spectrometer.frequency(id=data[i][0], frq=800, units='MHz')
# Clustering.
relax_disp.cluster(cluster_id='cluster', spin_id='@N,NE1')
# Set some parameters to speed up the optimisation.
value.set(param='kex', val=1500.0) # Real value of 1000.
# Auto-analysis execution.
##########################
# Run faster.
Relax_disp.opt_func_tol = 1e-10
Relax_disp.opt_max_iterations = 10000
# Do not change!
Relax_disp(pipe_name=pipe_name,
pipe_bundle=pipe_bundle,
results_dir=ds.tmpdir,
models=MODELS,
grid_inc=GRID_INC,
mc_sim_num=MC_NUM,
exp_mc_sim_num=EXP_MC_NUM)
# Save the program state.
state.save('devnull', force=True)
