Author: tlinnet
Date: Wed Aug 27 23:45:19 2014
New Revision: 25359
URL: http://svn.gna.org/viewcvs/relax?rev=25359&view=rev
Log:
Added script, to be used in GUI test.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
Added:
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py
Added:
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py?rev=25359&view=auto
==============================================================================
---
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py
(added)
+++
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py
Wed Aug 27 23:45:19 2014
@@ -0,0 +1,107 @@
+###############################################################################
+#
#
+# Copyright (C) 2013-2014 Troels E. Linnet
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Python module imports.
+from os import getcwd, sep
+
+# relax module imports.
+from status import Status; status = Status()
+
+#data_path = getcwd()
+data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
+
+# Read the spins.
+spectrum.read_spins(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
+
+# Name the isotope for field strength scaling.
+spin.isotope(isotope='15N')
+
+# Load the experiments settings file.
+expfile = open(data_path+sep+'exp_parameters_sort.txt', 'r')
+expfileslines = expfile.readlines()
+expfile.close()
+
+# In MHz
+yOBS = 81.050
+# In ppm
+yCAR = 118.078
+centerPPM_N15 = yCAR
+
+## Read the chemical shift data.
+chemical_shift.read(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
+
+## 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.
+ 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.
+ spectrum.baseplane_rmsd(error=apod_rmsd, spectrum_id=sp_id)
+
+ # Set the relaxation dispersion experiment type.
+ relax_disp.exp_type(spectrum_id=sp_id, exp_type='R1rho')
+
+ # Set The spin-lock field strength, nu1, in Hz
+ 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.
+ relax_disp.spin_lock_offset(spectrum_id=sp_id, offset=omega_rf_ppm)
+
+ # Set the relaxation times (in s).
+ relax_disp.relax_time(spectrum_id=sp_id, time=time_sl)
+
+ # Set the spectrometer frequency.
+ spectrometer.frequency(id=sp_id, frq=set_sfrq, units='MHz')
+
+
+# Read the R1 data
+# relax_data.read(ri_id='R1', ri_type='R1',
frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', 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)
r25359 - /trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py