Author: tlinnet
Date: Wed Aug 13 21:56:08 2014
New Revision: 25016
URL: http://svn.gna.org/viewcvs/relax?rev=25016&view=rev
Log:
Removed un-used scripts in folder of Kjaergaard et al., 2013.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
Removed:
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/omega_rf_ppm.txt
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/pipe_names_rx.txt
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/relax_2_spins.py
Removed:
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/omega_rf_ppm.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/omega_rf_ppm.txt?rev=25015&view=auto
==============================================================================
---
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/omega_rf_ppm.txt
(original)
+++
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/omega_rf_ppm.txt
(removed)
@@ -1,68 +0,0 @@
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 0.0 118.078
-81050000.0 118.078 6.16903146206 124.247031462
-81050000.0 118.078 6.16903146206 124.247031462
-81050000.0 118.078 6.16903146206 124.247031462
-81050000.0 118.078 6.16903146206 124.247031462
-81050000.0 118.078 6.16903146206 124.247031462
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 12.3380629241 130.416062924
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 24.6761258482 142.754125848
-81050000.0 118.078 61.6903146206 179.768314621
-81050000.0 118.078 61.6903146206 179.768314621
-81050000.0 118.078 61.6903146206 179.768314621
-81050000.0 118.078 61.6903146206 179.768314621
-81050000.0 118.078 61.6903146206 179.768314621
-81050000.0 118.078 123.380629241 241.458629241
-81050000.0 118.078 123.380629241 241.458629241
-81050000.0 118.078 123.380629241 241.458629241
-81050000.0 118.078 123.380629241 241.458629241
Removed:
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/pipe_names_rx.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/pipe_names_rx.txt?rev=25015&view=auto
==============================================================================
---
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/pipe_names_rx.txt
(original)
+++
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/pipe_names_rx.txt
(removed)
@@ -1,14 +0,0 @@
-0_35 relax_fit
-0_39 relax_fit
-0_41 relax_fit
-0_43 relax_fit
-0_46 relax_fit
-0_48 relax_fit
-500_46 relax_fit
-1000_41 relax_fit
-1000_46 relax_fit
-1000_48 relax_fit
-2000_41 relax_fit
-2000_46 relax_fit
-5000_46 relax_fit
-10000_46 relax_fit
Removed:
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py?rev=25015&view=auto
==============================================================================
---
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py
(original)
+++
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py
(removed)
@@ -1,28 +0,0 @@
-"""Taken from the relax disp manual, section 10.6.1 Dispersion script mode -
the sample script.
-Copyright (C) 2013 Troels E. Linnet
-
-To run the script, simply type:
-
-$ ../../../../../relax r1rho_1_ini.py --tee r1rho_1_ini.log
-"""
-
-# 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')
-
-# Create the spins
-spectrum.read_spins('peaks_corr_final.list')
-
-# Name the isotope for field strength scaling.
-spin.isotope(isotope='15N')
-
-## Read the chemical shift data.
-chemical_shift.read(file='peaks_corr_final.list', dir=None)
-
-# Set the spectra experimental properties/settings.
-script(file='r1rho_3_spectra_settings.py', dir=None)
-
-# Save the program state before run.
-# This state file will also be used for loading, before a later
cluster/global fit analysis.
-state.save('ini_setup_r1rho', force=True)
Removed:
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py?rev=25015&view=auto
==============================================================================
---
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py
(original)
+++
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py
(removed)
@@ -1,84 +0,0 @@
-# Copyright (C) 2013 Troels E. Linnet
-# Set settings for experiment
-import os
-
-NR_exp = -1
-
-# The lock power to field, has been found in an calibration experiment.
-# lock_powers = [35.0, 39.0, 41.0, 43.0, 46.0, 48.0]
-spin_lock_field_strengths_Hz = {'35': 431.0, '39': 651.2, '41': 800.5, '43':
984.0, '46': 1341.11, '48': 1648.5}
-ncycs = [0, 4, 10, 14, 20, 40]
-
-# Load the experiments settings file.
-expfile = open('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
-
-#gyro1H = 26.7522212E7
-#gyro15N = 2.7126E7
-
-writefile = open('omega_rf_ppm.txt', 'w')
-
-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])
- spin_lock_field_strength = spin_lock_field_strengths_Hz[dpwr2slock]
-
- # Calculate spin_lock time
- time_sl = 2*ncyc*trim
-
- # Load the R1 data.
- rxlabel = "%s_%s"%(deltadof2, dpwr2slock)
- rx_dir = os.path.join('rx', rxlabel)
- #relax_data.read(ri_id=rxlabel, ri_type='R1', frq=set_sfrq*1e6,
file='rx.out', dir=rx_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)
-
- # 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=os.path.join(os.getcwd(),
"peak_lists"), spectrum_id=sp_id, int_method='height')
-
- # Set the peak intensity errors, as defined as the baseplane RMSD.
- spectrum.baseplane_rmsd(error=1.33e+03, 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 = set_sfrq * 1E6 * gyro15N / gyro1H
- frq_N15_Hz = yOBS * 1E6
- offset_ppm_N15 = float(deltadof2) / frq_N15_Hz * 1E6
- omega_rf_ppm = centerPPM_N15 + offset_ppm_N15
- writefile.write("%s %s %s %s\n"%(frq_N15_Hz, centerPPM_N15,
offset_ppm_N15, omega_rf_ppm))
-
- # 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_fit.relax_time(time=time_sl, spectrum_id=sp_id)
-
- # Set the spectrometer frequency.
- spectrometer.frequency(id=sp_id, frq=set_sfrq, units='MHz')
-
-writefile.close()
Removed:
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py?rev=25015&view=auto
==============================================================================
---
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py
(original)
+++
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py
(removed)
@@ -1,34 +0,0 @@
-"""Taken from the relax disp manual, section 10.6.1 Dispersion script mode -
the sample script.
-# Copyright (C) 2013 Troels E. Linnet
-
-To run the script, simply type:
-
-$ ../../../../../relax r1rho_4_run.py --tee log_r1rho_4_run.log
-"""
-
-import os
-from auto_analyses.relax_disp import Relax_disp
-
-# Setting variables for pipe names.
-pipe_name = 'base pipe'
-pipe_bundle = 'relax_disp'
-
-# 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'
-
-# Load the initial state setup
-state.load(state='ini_setup_r1rho.bz2')
-
-# Run faster.
-Relax_disp.opt_func_tol = 1e-10
-Relax_disp.opt_max_iterations = 10000
-
-results_directory = os.path.join("r1rho", "test")
-
-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)
Removed:
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/relax_2_spins.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/relax_2_spins.py?rev=25015&view=auto
==============================================================================
---
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/relax_2_spins.py
(original)
+++
branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/relax_2_spins.py
(removed)
@@ -1,48 +0,0 @@
-spin.create(spin_name='N', spin_num=1, res_name='I', res_num=5,
mol_name=None)
-spin.create(spin_name='N', spin_num=2, res_name='S', res_num=6,
mol_name=None)
-spin.create(spin_name='N', spin_num=3, res_name='S', res_num=8,
mol_name=None)
-spin.create(spin_name='N', spin_num=4, res_name='A', res_num=9,
mol_name=None)
-spin.create(spin_name='N', spin_num=5, res_name='L', res_num=10,
mol_name=None)
-spin.create(spin_name='N', spin_num=6, res_name='Q', res_num=11,
mol_name=None)
-spin.create(spin_name='N', spin_num=7, res_name='D', res_num=12,
mol_name=None)
-spin.create(spin_name='N', spin_num=8, res_name='L', res_num=13,
mol_name=None)
-spin.create(spin_name='N', spin_num=9, res_name='L', res_num=14,
mol_name=None)
-spin.create(spin_name='N', spin_num=10, res_name='R', res_num=15,
mol_name=None)
-spin.create(spin_name='N', spin_num=11, res_name='T', res_num=16,
mol_name=None)
-spin.create(spin_name='N', spin_num=12, res_name='L', res_num=17,
mol_name=None)
-spin.create(spin_name='N', spin_num=13, res_name='K', res_num=18,
mol_name=None)
-spin.create(spin_name='N', spin_num=14, res_name='S', res_num=19,
mol_name=None)
-spin.create(spin_name='N', spin_num=15, res_name='S', res_num=21,
mol_name=None)
-spin.create(spin_name='N', spin_num=16, res_name='Q', res_num=24,
mol_name=None)
-spin.create(spin_name='N', spin_num=17, res_name='Q', res_num=25,
mol_name=None)
-spin.create(spin_name='N', spin_num=18, res_name='Q', res_num=26,
mol_name=None)
-spin.create(spin_name='N', spin_num=19, res_name='Q', res_num=27,
mol_name=None)
-spin.create(spin_name='N', spin_num=20, res_name='Q', res_num=28,
mol_name=None)
-spin.create(spin_name='N', spin_num=21, res_name='V', res_num=29,
mol_name=None)
-spin.create(spin_name='N', spin_num=22, res_name='L', res_num=30,
mol_name=None)
-spin.create(spin_name='N', spin_num=23, res_name='N', res_num=31,
mol_name=None)
-spin.create(spin_name='N', spin_num=24, res_name='I', res_num=32,
mol_name=None)
-spin.create(spin_name='N', spin_num=25, res_name='L', res_num=33,
mol_name=None)
-spin.create(spin_name='N', spin_num=26, res_name='K', res_num=34,
mol_name=None)
-spin.create(spin_name='N', spin_num=27, res_name='S', res_num=35,
mol_name=None)
-spin.create(spin_name='N', spin_num=28, res_name='N', res_num=36,
mol_name=None)
-spin.create(spin_name='N', spin_num=29, res_name='Q', res_num=38,
mol_name=None)
-spin.create(spin_name='N', spin_num=30, res_name='L', res_num=39,
mol_name=None)
-spin.create(spin_name='N', spin_num=31, res_name='M', res_num=40,
mol_name=None)
-spin.create(spin_name='N', spin_num=32, res_name='A', res_num=41,
mol_name=None)
-spin.create(spin_name='N', spin_num=33, res_name='A', res_num=42,
mol_name=None)
-spin.create(spin_name='N', spin_num=34, res_name='F', res_num=43,
mol_name=None)
-spin.create(spin_name='N', spin_num=35, res_name='I', res_num=44,
mol_name=None)
-spin.create(spin_name='N', spin_num=36, res_name='K', res_num=45,
mol_name=None)
-spin.create(spin_name='N', spin_num=37, res_name='Q', res_num=46,
mol_name=None)
-spin.create(spin_name='N', spin_num=38, res_name='T', res_num=48,
mol_name=None)
-spin.create(spin_name='N', spin_num=39, res_name='A', res_num=49,
mol_name=None)
-spin.create(spin_name='N', spin_num=40, res_name='K', res_num=50,
mol_name=None)
-spin.create(spin_name='N', spin_num=41, res_name='Y', res_num=51,
mol_name=None)
-spin.create(spin_name='N', spin_num=42, res_name='V', res_num=52,
mol_name=None)
-spin.create(spin_name='N', spin_num=43, res_name='A', res_num=53,
mol_name=None)
-spin.create(spin_name='N', spin_num=44, res_name='N', res_num=54,
mol_name=None)
-spin.create(spin_name='N', spin_num=45, res_name='Q', res_num=55,
mol_name=None)
-spin.create(spin_name='N', spin_num=46, res_name='G', res_num=57,
mol_name=None)
-spin.create(spin_name='N', spin_num=47, res_name='M', res_num=58,
mol_name=None)
-spin.create(spin_name='N', spin_num=48, res_name='Q', res_num=59,
mol_name=None)
r25016 - /branches/R1_fitting/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/