Author: bugman
Date: Tue Apr 16 11:15:32 2013
New Revision: 19485
URL: http://svn.gna.org/viewcvs/relax?rev=19485&view=rev
Log:
Updated the dispersion system test script for Flemming Hansen's data.
This script should now be close to the final form for a relaxation dispersion
analysis of CPMG data
with a fixed relaxation time period.
Modified:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data_fast_2site.py
Modified:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data_fast_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data_fast_2site.py?rev=19485&r1=19484&r2=19485&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data_fast_2site.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data_fast_2site.py
Tue Apr 16 11:15:32 2013
@@ -1,132 +1,130 @@
-# Script for CPMG relaxation dispersion curve fitting in the fast-exchange
limit.
+# 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 = ['exp_fit', '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
+
+
+
+# Set up the data pipe.
+#######################
+
+# The results directory.
+if not hasattr(ds, 'tmpdir'):
+ ds.tmpdir = None
+
# Create the data pipe.
-pipe.create('rex', 'relax_disp')
+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_path1 = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'500_MHz'
-data_path2 = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'800_MHz'
+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+'curve_fitting_disp'+sep+'Hansen',
res_num_col=1, res_name_col=2)
+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')
+relax_disp.exp_type('cpmg fixed')
-# Set the relaxation dispersion curve type.
-relax_disp.select_model('fast')
-
-# Relaxation dispersion magnetic field (in Hz).
-frq.set(id='500', frq=500.0 * 1e6)
-frq.set(id='800', frq=800.0 * 1e6)
-
-# Spectrum names.
-names = [
- 'reference.in_sparky',
- '66.667.in_sparky',
- '1000.in_sparky',
- '133.33.in_sparky',
- '933.33.in_sparky',
- '200.in_sparky',
- '866.67.in_sparky',
- '266.67.in_sparky',
- '800.in_sparky',
- '333.33.in_sparky',
- '733.33.in_sparky',
- '400.in_sparky',
- '666.67.in_sparky',
- '466.67.in_sparky',
- '600.in_sparky',
- '533.33.in_sparky',
- '133.33.in.bis_sparky',
- '933.33.in.bis_sparky',
- '533.33.in.bis_sparky'
-]
-
-# Relaxation dispersion CPMG constant time delay T (in s).
-relax_disp.cpmg_delayT(id='500', delayT=0.030)
-relax_disp.cpmg_delayT(id='800', delayT=0.030)
-
-# Relaxation dispersion CPMG frequencies (in Hz).
-cpmg_frq = [
- None,
- 66.667,
- 1000,
- 133.33,
- 933.33,
- 200,
- 866.67,
- 266.67,
- 800,
- 333.33,
- 733.33,
- 400,
- 666.67,
- 466.67,
- 600,
- 533.33,
- 133.33,
- 933.33,
- 533.33
+# 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 i in xrange(len(names)):
+for id, file, cpmg_frq, H_frq in data:
# Load the peak intensities.
- spectrum.read_intensities(file=names[i], dir=data_path1,
spectrum_id=names[i], int_method='height')
- spectrum.read_intensities(file=names[i], dir=data_path2,
spectrum_id=names[i], int_method='height')
+ spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id,
int_method='height')
+
+ # Relaxation dispersion CPMG constant time delay T (in s).
+ relax_disp.cpmg_delayT(spectrum_id=id, delayT=0.030)
# Set the relaxation dispersion CPMG frequencies.
- relax_disp.cpmg_frq(cpmg_frq=cpmg_frq[i], spectrum_id=names[i])
+ 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)
# Specify the duplicated spectra.
-spectrum.replicated(spectrum_ids=['133.33.in_sparky',
'133.33.in.bis_sparky'])
-spectrum.replicated(spectrum_ids=['533.33.in_sparky',
'533.33.in.bis_sparky'])
-spectrum.replicated(spectrum_ids=['933.33.in_sparky',
'933.33.in.bis_sparky'])
+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()
+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_path1, res_num_col=1)
-deselect.read(file='unresolved', dir=data_path2, res_num_col=1)
+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)
-# Grid search.
-grid_search(inc=11)
-# Minimise.
-minimise('simplex', constraints=False)
+# Auto-analysis execution.
+##########################
-# Monte Carlo simulations.
-monte_carlo.setup(number=10)
-monte_carlo.create_data()
-monte_carlo.initial_values()
-minimise('simplex', constraints=False)
-monte_carlo.error_analysis()
-
-# Save the relaxation dispersion parameters.
-value.write(param='rex', file='devnull', force=True)
-
-# Save the results.
-results.write(file='devnull', force=True)
-
-# Create Grace plots of the data.
-grace.write(y_data_type='chi2', file='devnull', force=True) # Minimised
chi-squared value.
-grace.write(y_data_type='R2', file='devnull', force=True) # R2 parameter
without Rex contribution.
-grace.write(y_data_type='Rex', file='devnull', force=True) # Chemical
exchange contribution to observed R2.
-grace.write(y_data_type='kex', file='devnull', force=True) # Exchange
rate.
-grace.write(x_data_type='frq', y_data_type='int', file='devnull',
force=True) # Average peak intensities.
-grace.write(x_data_type='frq', y_data_type='int', norm=True, file='devnull',
force=True) # Average peak intensities (normalised).
+# 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)
# Save the program state.
state.save('devnull', force=True)
r19485 - /branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data_fast_2site.py