Author: bugman
Date: Thu Apr 11 12:43:52 2013
New Revision: 19454
URL: http://svn.gna.org/viewcvs/relax?rev=19454&view=rev
Log:
Rearrangements of the 2 system tests of Fleming Hansen's CPMG data.
The system tests are now called Relax_disp.test_hansen_cpmg_data_fast_2site
and
Relax_disp.test_hansen_cpmg_data_slow_2site, and the system test scripts are
now all in
test_suite/system_tests/scripts/relax_disp/.
Added:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data_fast_2site.py
- copied unchanged from r19452,
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data_slow_2site.py
- copied unchanged from r19452,
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
Removed:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
Modified:
branches/relax_disp/test_suite/system_tests/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=19454&r1=19453&r2=19454&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Thu Apr 11
12:43:52 2013
@@ -55,20 +55,18 @@
ds.__reset__()
- def test_curve_fitting_cpmg_fast(self):
- """Test the relaxation dispersion curve fitting C modules for CPMG
data in the
- fast-exchange limit."""
+ def test_hansen_cpmg_data_fast_2site(self):
+ """Optimisation of Fleming Hansen's CPMG data to the fast 2-site
dispersion model."""
# Execute the script.
- self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp_cpmg_fast.py')
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data_fast_2site.py')
- def test_curve_fitting_cpmg_slow(self):
- """Test the relaxation dispersion curve fitting C modules for CPMG
data in the
- slow-exchange limit."""
+ def test_hansen_cpmg_data_slow_2site(self):
+ """Optimisation of Fleming Hansen's CPMG data to the slow 2-site
dispersion model."""
# Execute the script.
- self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp_cpmg_slow.py')
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data_slow_2site.py')
def test_exp_fit(self):
Removed:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py?rev=19453&view=auto
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
(removed)
@@ -1,132 +1,0 @@
-# Script for CPMG relaxation dispersion curve fitting in the fast-exchange
limit.
-
-# Python module imports.
-from os import sep
-
-# relax module imports.
-from status import Status; status = Status()
-
-
-# Create the data pipe.
-pipe.create('rex', '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'
-
-# 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)
-
-# 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')
-
-# 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
-]
-
-# Loop over the spectra.
-for i in xrange(len(names)):
- # 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')
-
- # Set the relaxation dispersion CPMG frequencies.
- relax_disp.cpmg_frq(cpmg_frq=cpmg_frq[i], spectrum_id=names[i])
-
-# 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'])
-
-# Peak intensity error analysis.
-spectrum.error_analysis()
-
-# 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)
-
-# 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 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).
-
-# Save the program state.
-state.save('devnull', force=True)
Removed:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py?rev=19453&view=auto
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
(removed)
@@ -1,127 +1,0 @@
-# Script for CPMG relaxation dispersion curve fitting in the slow-exchange
limit.
-
-# Python module imports.
-from os import sep
-
-# relax module imports.
-from status import Status; status = Status()
-
-
-# Create the data pipe.
-pipe.create('rex', 'relax_disp')
-
-# The path to the data files.
-data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'500_MHz'
-
-# 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)
-
-# 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')
-
-# Set the relaxation dispersion curve type.
-relax_disp.select_model('slow')
-
-# Relaxation dispersion magnetic field (in Hz).
-frq.set(id='500', frq=500.0 * 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)
-
-# 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
-]
-
-# Loop over the spectra.
-for i in xrange(len(names)):
- # Load the peak intensities.
- spectrum.read_intensities(file=names[i], dir=data_path,
spectrum_id=names[i], int_method='height')
-
- # Set the relaxation dispersion CPMG frequencies.
- relax_disp.cpmg_frq(cpmg_frq=cpmg_frq[i], spectrum_id=names[i])
-
-# 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'])
-
-# Peak intensity error analysis.
-spectrum.error_analysis()
-
-# Deselect unresolved spins.
-deselect.read(file='unresolved', dir=data_path, res_num_col=1)
-
-# 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 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).
-
-# Save the program state.
-state.save('devnull', force=True)
r19454 - in /branches/relax_disp/test_suite/system_tests: ./ scripts/ scripts/relax_disp/