Author: semor
Date: Wed Jan 7 22:16:16 2009
New Revision: 8324
URL: http://svn.gna.org/viewcvs/relax?rev=8324&view=rev
Log:
Modified the script so it will test for fast-exchange curve fitting from CPMG
data.
Data and functions to treat it arestill missing.
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=8324&r1=8323&r2=8324&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Wed Jan 7
22:16:16 2009
@@ -59,8 +59,9 @@
ds.__reset__()
- def test_curve_fitting(self):
- """Test the relaxation dispersion curve fitting C modules."""
+ def test_curve_fitting_cpmg_fast(self):
+ """Test the relaxation dispersion curve fitting C modules for CPMG
data in the
+ fast-exchange limit."""
# Execute the script.
self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/relax_disp.py')
Modified: 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=8324&r1=8323&r2=8324&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py
(original)
+++ branches/relax_disp/test_suite/system_tests/scripts/relax_disp.py Wed Jan
7 22:16:16 2009
@@ -1,13 +1,13 @@
-# Script for relaxation curve fitting.
+# Script for CPMG relaxation dispersion curve fitting in the fast-exchange
limit.
import sys
# Create the data pipe.
-pipe.create('rx', 'relax_fit')
+pipe.create('rex', 'relax_disp')
# The path to the data files.
-data_path = sys.path[-1] + '/test_suite/shared_data/curve_fitting'
+data_path = sys.path[-1] + '/test_suite/shared_data/disp_curve_fitting'
# Load the sequence.
sequence.read('Ap4Aase.seq', dir=sys.path[-1] + '/test_suite/shared_data')
@@ -15,56 +15,40 @@
# 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'
-]
+## Spectrum names.
+#names = [
+# 'T2_ncyc1_ave',
+# 'T2_ncyc11b_ave'
+#]
+#
+## Relaxation dispersion CPMG frequencies (in Hz).
+#frq = [
+# 0.0176,
+# 0.1936
+#]
-# 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
-]
+# Set the relaxation dispersion experiment type.
+relax_disp.exp_type('cpmg')
+
+# Set the relaxation dispersion curve type.
+relax_disp.select_model('fast')
# 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])
+ # Set the relaxation dispersion CPMG frequencies.
+ relax_disp.relax_time(frq=frq[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'])
+#spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_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)
@@ -79,18 +63,19 @@
minimise('simplex', constraints=False)
monte_carlo.error_analysis()
-# Save the relaxation rates.
-value.write(param='rx', file='devnull', force=True)
+# 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='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).
+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).
# Save the program state.
state.save('devnull', force=True)
r8324 - in /branches/relax_disp/test_suite/system_tests: relax_disp.py scripts/relax_disp.py