Author: tlinnet
Date: Mon Dec 9 17:49:49 2013
New Revision: 21920
URL: http://svn.gna.org/viewcvs/relax?rev=21920&view=rev
Log:
Added system test for the analysis of optimisation of the Kjaergaard et al.,
2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL'
model.
Work in progress for Support Request #3083,
(https://gna.org/support/index.php?3083) - Addition of Data-set for R1rho
analysis.
Modified:
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21920&r1=21919&r2=21920&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Dec 9 17:49:49 2013
@@ -2450,6 +2450,137 @@
self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2,
0.030959849811015544, 3)
+ def test_r1rho_kjaergaard(self):
+ """Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho
relaxation dispersion experiments using the 'DPL' model.
+
+ This uses the data from Kjaergaard's paper at U{DOI:
10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}.
+
+ """
+
+ # The path to the data files.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
+
+ # Set pipe name, bundle and type.
+ pipe_name = 'base pipe'
+ pipe_bundle = 'relax_disp'
+ pipe_type= 'relax_disp'
+
+ # Create the data pipe.
+ self.interpreter.pipe.create(pipe_name=pipe_name,
bundle=pipe_bundle, pipe_type=pipe_type)
+
+ # Read the spins.
+
self.interpreter.spectrum.read_spins(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
+
+ # Test some of the sequence.
+ self.assertEqual(len(cdp.mol), 1)
+ self.assertEqual(cdp.mol[0].name, None)
+ self.assertEqual(len(cdp.mol[0].res), 48)
+
+ # Name the isotope for field strength scaling.
+ self.interpreter.spin.isotope(isotope='15N')
+
+ # Set number of experiments to be used.
+ NR_exp = -1
+
+ # Load the experiments settings file.
+ expfile = open(data_path+sep+'exp_parameters_sort.txt','r')
+ expfileslines = expfile.readlines()[:NR_exp]
+ expfile.close()
+
+ # In MHz
+ yOBS = 81.050
+ # In ppm
+ yCAR = 118.078
+ centerPPM_N15 = yCAR
+
+ ## Read the chemical shift data.
+
self.interpreter.chemical_shift.read(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
+
+ # Test the chemical shift data.
+ cs = [122.223, 122.162, 114.250, 125.852, 118.626, 117.449, 119.999,
122.610, 118.602, 118.291, 115.393,
+ 121.288, 117.448, 116.378, 116.316, 117.263, 122.211, 118.748,
118.103, 119.421, 119.317, 119.386, 117.279,
+ 122.103, 120.038, 116.698, 111.811, 118.639, 118.285, 121.318,
117.770, 119.948, 119.759, 118.314, 118.160,
+ 121.442, 118.714, 113.080, 125.706, 119.183, 120.966, 122.361,
126.675, 117.069, 120.875, 109.372, 119.811, 126.048]
+
+ i = 0
+ for spin, spin_id in spin_loop(return_id=True):
+ print spin.name, spin.num, spin_id, spin.chemical_shift, cs[i]
+ # Check the chemical shift.
+ self.assertEqual(spin.chemical_shift, cs[i])
+
+ # Increment the index.
+ i += 1
+
+ # The lock power to field, has been found in an calibration
experiment.
+ spin_lock_field_strengths_Hz = {'35': 431.0, '39': 651.2, '41':
800.5, '43': 984.0, '46': 1341.11, '48': 1648.5}
+
+ # Apply spectra settings.
+ for i in range(len(expfileslines)):
+ line=expfileslines[i]
+ if line[0] == "#":
+ continue
+ else:
+ # DIRN I deltadof2 dpwr2slock ncyc trim ss sfrq
+ DIRN = line.split()[0]
+ I = int(line.split()[1])
+ deltadof2 = line.split()[2]
+ dpwr2slock = line.split()[3]
+ ncyc = int(line.split()[4])
+ trim = float(line.split()[5])
+ ss = int(line.split()[6])
+ set_sfrq = float(line.split()[7])
+ apod_rmsd = float(line.split()[8])
+ spin_lock_field_strength =
spin_lock_field_strengths_Hz[dpwr2slock]
+
+ # Calculate spin_lock time
+ time_sl = 2*ncyc*trim
+
+ # Define file name for peak list.
+ FNAME = "%s_%s_%s_%s_max_standard.ser"%(I, deltadof2,
dpwr2slock, ncyc)
+ sp_id = "%s_%s_%s_%s"%(I, deltadof2, dpwr2slock, ncyc)
+
+ # Load the peak intensities.
+ self.interpreter.spectrum.read_intensities(file=FNAME,
dir=data_path+sep+'peak_lists', spectrum_id=sp_id, int_method='height')
+
+ # Set the peak intensity errors, as defined as the baseplane
RMSD.
+ self.interpreter.spectrum.baseplane_rmsd(error=apod_rmsd,
spectrum_id=sp_id)
+
+ # Set the relaxation dispersion experiment type.
+ self.interpreter.relax_disp.exp_type(spectrum_id=sp_id,
exp_type='R1rho')
+
+ # Set The spin-lock field strength, nu1, in Hz
+
self.interpreter.relax_disp.spin_lock_field(spectrum_id=sp_id,
field=spin_lock_field_strength)
+
+ # Calculating the spin-lock offset in ppm, from offsets
values provided in Hz.
+ frq_N15_Hz = yOBS * 1E6
+ offset_ppm_N15 = float(deltadof2) / frq_N15_Hz * 1E6
+ omega_rf_ppm = centerPPM_N15 + offset_ppm_N15
+
+ # Set The spin-lock offset, omega_rf, in ppm.
+
self.interpreter.relax_disp.spin_lock_offset(spectrum_id=sp_id,
offset=omega_rf_ppm)
+
+ # Set the relaxation times (in s).
+ self.interpreter.relax_fit.relax_time(time=time_sl,
spectrum_id=sp_id)
+
+ # Set the spectrometer frequency.
+ self.interpreter.spectrometer.frequency(id=sp_id,
frq=set_sfrq, units='MHz')
+
+ # The dispersion models.
+ MODELS = ['R2eff', 'No Rex', 'DPL94']
+
+ # The grid search size (the number of increments per dimension).
+ GRID_INC = 4
+
+ # The number of Monte Carlo simulations to be used for error
analysis at the end of the analysis.
+ MC_NUM = 3
+
+ # Model selection technique.
+ MODSEL = 'AIC'
+
+ # Run the analysis.
+ relax_disp.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)
+
+
def test_r2eff_read(self):
"""Test the operation of the relax_disp.r2eff_read user function."""
r21920 - /trunk/test_suite/system_tests/relax_disp.py