Author: semor
Date: Tue Jan 6 20:07:10 2009
New Revision: 8229
URL: http://svn.gna.org/viewcvs/relax?rev=8229&view=rev
Log:
Added a directory and a script for relaxation dispersion curve fitting
system tests.
The next step will be to find published data to use in the tests. We will
need data for the three
cases of slow-, intermediate-, and fast-exchange...
Added:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py
Added: branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py?rev=8229&view=auto
==============================================================================
--- branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py
(added)
+++ branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py Tue
Jan 6 20:07:10 2009
@@ -1,0 +1,96 @@
+# Script for relaxation curve fitting.
+
+import sys
+
+
+# Create the data pipe.
+pipe.create('rx', 'relax_disp')
+
+# The path to the data files.
+data_path = sys.path[-1] + '/test_suite/shared_data/relax_disp'
+
+## Load the sequence.
+#sequence.read('Ap4Aase.seq', dir=sys.path[-1] +
'/test_suite/shared_data')
+#
+## Name the spins so they can be matched to the assignments.
+#spin.name(name='N')
+#
+## Spectrum names.
+#names = [
+# 'T2_ncyc1_ave',
+# 'T2_ncyc1b_ave',
+# 'T2_ncyc2_ave',
+# 'T2_ncyc4_ave',
+# 'T2_ncyc4b_ave',
+# 'T2_ncyc6_ave',
+# 'T2_ncyc9_ave',
+# 'T2_ncyc9b_ave',
+# 'T2_ncyc11_ave',
+# 'T2_ncyc11b_ave'
+#]
+#
+## Relaxation times (in seconds).
+#times = [
+# 0.0176,
+# 0.0176,
+# 0.0352,
+# 0.0704,
+# 0.0704,
+# 0.1056,
+# 0.1584,
+# 0.1584,
+# 0.1936,
+# 0.1936
+#]
+#
+## Loop over the spectra.
+#for i in xrange(len(names)):
+# # Load the peak intensities.
+# spectrum.read_intensities(file=names[i]+'.list', dir=data_path,
spectrum_id=names[i], int_method='height')
+#
+# # Set the relaxation times.
+# relax_fit.relax_time(time=times[i], spectrum_id=names[i])
+#
+## Specify the duplicated spectra.
+#spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
+#spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
+#spectrum.replicated(spectrum_ids=['T2_ncyc9_ave', 'T2_ncyc9b_ave'])
+#spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
+#
+## Peak intensity error analysis.
+#spectrum.error_analysis()
+#
+## Deselect unresolved spins.
+#deselect.read(file='unresolved', dir=data_path)
+#
+## Set the relaxation curve type.
+#relax_fit.select_model('exp')
+#
+## Grid search.
+#grid_search(inc=11)
+#
+## Minimise.
+#minimise('simplex', constraints=False)
+#
+## 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 rates.
+#value.write(param='rx', 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='i0', file='devnull', force=True) # Initial
peak intensity.
+#grace.write(y_data_type='rx', file='devnull', force=True) #
Relaxation rate.
+#grace.write(x_data_type='relax_times', y_data_type='int',
file='devnull', force=True) # Average peak intensities.
+#grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='devnull', force=True) # Average peak intensities (normalised).
+#
+## Save the program state.
+#state.save('devnull', force=True)
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