Author: bugman
Date: Fri May 3 15:45:38 2013
New Revision: 19636
URL: http://svn.gna.org/viewcvs/relax?rev=19636&view=rev
Log:
Created a script for running a full relaxation dispersion analysis on
Flemming Hansen's data.
This is located in the shared data directories and is not part of the test
suite as a full analysis
will take far too long.
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/relax_disp.py
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/relax_disp.py?rev=19636&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/relax_disp.py
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/relax_disp.py
Fri May 3 15:45:38 2013
@@ -1,0 +1,128 @@
+# Script for CPMG relaxation dispersion curve fitting using Dr. Flemming
Hansen's data from http://dx.doi.org/10.1021/jp074793o.
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from auto_analyses.relax_disp import Relax_disp
+from data_store import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
+
+
+# Analysis variables.
+#####################
+
+# The dispersion models.
+MODELS = ['R2eff', 'fast 2-site']
+
+# The grid search size (the number of increments per dimension).
+GRID_INC = 5
+
+# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
+MC_NUM = 3
+
+# The results directory.
+RESULTS_DIR = 'temp'
+
+
+# Set up the data pipe.
+#######################
+
+# 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 sequence.
+sequence.read('fake_sequence.in', dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen',
res_num_col=1, res_name_col=2)
+
+# Name the spins so they can be matched to the assignments.
+spin.name(name='N')
+
+# Set the relaxation dispersion experiment type.
+relax_disp.exp_type('cpmg fixed')
+
+# The spectral data - spectrum ID, peak list file name, CPMG frequency (Hz),
spectrometer frequency in Hertz.
+data = [
+ ['500_reference.in', '500_MHz'+sep+'reference.in_sparky',
None, 500e6],
+ ['500_66.667.in', '500_MHz'+sep+'66.667.in_sparky',
66.6666, 500e6],
+ ['500_133.33.in', '500_MHz'+sep+'133.33.in_sparky',
133.3333, 500e6],
+ ['500_133.33.in.bis', '500_MHz'+sep+'133.33.in.bis_sparky',
133.3333, 500e6],
+ ['500_200.in', '500_MHz'+sep+'200.in_sparky',
200.0000, 500e6],
+ ['500_266.67.in', '500_MHz'+sep+'266.67.in_sparky',
266.6666, 500e6],
+ ['500_333.33.in', '500_MHz'+sep+'333.33.in_sparky',
333.3333, 500e6],
+ ['500_400.in', '500_MHz'+sep+'400.in_sparky',
400.0000, 500e6],
+ ['500_466.67.in', '500_MHz'+sep+'466.67.in_sparky',
466.6666, 500e6],
+ ['500_533.33.in', '500_MHz'+sep+'533.33.in_sparky',
533.3333, 500e6],
+ ['500_533.33.in.bis', '500_MHz'+sep+'533.33.in.bis_sparky',
533.3333, 500e6],
+ ['500_600.in', '500_MHz'+sep+'600.in_sparky',
600.0000, 500e6],
+ ['500_666.67.in', '500_MHz'+sep+'666.67.in_sparky',
666.6666, 500e6],
+ ['500_733.33.in', '500_MHz'+sep+'733.33.in_sparky',
733.3333, 500e6],
+ ['500_800.in', '500_MHz'+sep+'800.in_sparky',
800.0000, 500e6],
+ ['500_866.67.in', '500_MHz'+sep+'866.67.in_sparky',
866.6666, 500e6],
+ ['500_933.33.in', '500_MHz'+sep+'933.33.in_sparky',
933.3333, 500e6],
+ ['500_933.33.in.bis', '500_MHz'+sep+'933.33.in.bis_sparky',
933.3333, 500e6],
+ ['500_1000.in', '500_MHz'+sep+'1000.in_sparky',
1000.0000, 500e6],
+ ['800_reference.in', '800_MHz'+sep+'reference.in_sparky',
None, 800e6],
+ ['800_66.667.in', '800_MHz'+sep+'66.667.in_sparky',
66.6666, 800e6],
+ ['800_133.33.in', '800_MHz'+sep+'133.33.in_sparky',
133.3333, 800e6],
+ ['800_133.33.in.bis', '800_MHz'+sep+'133.33.in.bis_sparky',
133.3333, 800e6],
+ ['800_200.in', '800_MHz'+sep+'200.in_sparky',
200.0000, 800e6],
+ ['800_266.67.in', '800_MHz'+sep+'266.67.in_sparky',
266.6666, 800e6],
+ ['800_333.33.in', '800_MHz'+sep+'333.33.in_sparky',
333.3333, 800e6],
+ ['800_400.in', '800_MHz'+sep+'400.in_sparky',
400.0000, 800e6],
+ ['800_466.67.in', '800_MHz'+sep+'466.67.in_sparky',
466.6666, 800e6],
+ ['800_533.33.in', '800_MHz'+sep+'533.33.in_sparky',
533.3333, 800e6],
+ ['800_533.33.in.bis', '800_MHz'+sep+'533.33.in.bis_sparky',
533.3333, 800e6],
+ ['800_600.in', '800_MHz'+sep+'600.in_sparky',
600.0000, 800e6],
+ ['800_666.67.in', '800_MHz'+sep+'666.67.in_sparky',
666.6666, 800e6],
+ ['800_733.33.in', '800_MHz'+sep+'733.33.in_sparky',
733.3333, 800e6],
+ ['800_800.in', '800_MHz'+sep+'800.in_sparky',
800.0000, 800e6],
+ ['800_866.67.in', '800_MHz'+sep+'866.67.in_sparky',
866.6666, 800e6],
+ ['800_933.33.in', '800_MHz'+sep+'933.33.in_sparky',
933.3333, 800e6],
+ ['800_933.33.in.bis', '800_MHz'+sep+'933.33.in.bis_sparky',
933.3333, 800e6],
+ ['800_1000.in', '800_MHz'+sep+'1000.in_sparky',
1000.0000, 800e6]
+]
+
+# Loop over the spectra.
+for id, file, cpmg_frq, H_frq in data:
+ # Load the peak intensities.
+ spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id,
int_method='height')
+
+ # Set the relaxation dispersion CPMG frequencies.
+ relax_disp.cpmg_frq(spectrum_id=id, cpmg_frq=cpmg_frq)
+
+ # Set the NMR field strength of the spectrum.
+ frq.set(id=id, frq=H_frq)
+
+ # Relaxation dispersion CPMG constant time delay T (in s).
+ relax_disp.relax_time(spectrum_id=id, time=0.030)
+
+# Specify the duplicated spectra.
+spectrum.replicated(spectrum_ids=['500_133.33.in', '500_133.33.in.bis'])
+spectrum.replicated(spectrum_ids=['500_533.33.in', '500_533.33.in.bis'])
+spectrum.replicated(spectrum_ids=['500_933.33.in', '500_933.33.in.bis'])
+spectrum.replicated(spectrum_ids=['800_133.33.in', '800_133.33.in.bis'])
+spectrum.replicated(spectrum_ids=['800_533.33.in', '800_533.33.in.bis'])
+spectrum.replicated(spectrum_ids=['800_933.33.in', '800_933.33.in.bis'])
+
+# Peak intensity error analysis.
+spectrum.error_analysis(subset=['500_reference.in', '500_66.667.in',
'500_133.33.in', '500_133.33.in.bis', '500_200.in', '500_266.67.in',
'500_333.33.in', '500_400.in', '500_466.67.in', '500_533.33.in',
'500_533.33.in.bis', '500_600.in', '500_666.67.in', '500_733.33.in',
'500_800.in', '500_866.67.in', '500_933.33.in', '500_933.33.in.bis',
'500_1000.in'])
+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)
+
+
+# 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)
+
+# Save the program state.
+state.save('state', force=True)
r19636 - /branches/relax_disp/test_suite/shared_data/dispersion/Hansen/relax_disp.py