Author: bugman
Date: Sun Jun 9 10:52:44 2013
New Revision: 19985
URL: http://svn.gna.org/viewcvs/relax?rev=19985&view=rev
Log:
Created the Relax_disp.test_r1rho_on_res_fixed_time_m61b system test.
This is for the Meiboom 1961 on-resonance 2-site model for skewed populations
(pA >> pB).
This commit follows step 7 of the relaxation dispersion model addition
tutorial
(http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
Added:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61b.py
- copied, changed from r19979,
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.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=19985&r1=19984&r2=19985&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Sun Jun 9
10:52:44 2013
@@ -29,7 +29,7 @@
from auto_analyses import relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from pipe_control.mol_res_spin import spin_loop
-from specific_analyses.relax_disp.variables import MODEL_LIST_CPMG
+from specific_analyses.relax_disp.variables import MODEL_LIST_CPMG,
MODEL_M61B, MODEL_R2EFF
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -562,3 +562,49 @@
# Increment the spin index.
spin_index += 1
+
+
+ def test_r1rho_on_res_fixed_time_m61b(self):
+ """Test the relaxation dispersion 'M61 skew' model curve fitting to
fixed time synthetic data."""
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_on_res_m61b.py')
+
+ # The original parameters.
+ i0 = [100000.0, 20000.0]
+ r1rho_prime = [2.25, 24.0]
+ pA = 0.95
+ kex = 2000.0
+ delta_omega = [1.0, 2.0]
+ keys = ['800.0_1000.0', '800.0_1500.0', '800.0_2000.0',
'800.0_2500.0', '800.0_3000.0', '800.0_3500.0', '800.0_4000.0',
'800.0_4500.0', '800.0_5000.0', '800.0_5500.0', '800.0_6000.0']
+ rates = [[3.59768160399, 2.85730469783, 2.59328084312,
2.47019857325, 2.40310451058, 2.36256876552, 2.33622716364, 2.31815271355,
2.30521680479, 2.29564174079, 2.28835686631], [29.390726416, 26.4292187913,
25.3731233725, 24.880794293, 24.6124180423, 24.4502750621, 24.3449086546,
24.2726108542, 24.2208672192, 24.1825669632, 24.1534274652]]
+
+ # Switch to the 'R2eff' model data pipe, then check for each spin.
+ self.interpreter.pipe.switch(MODEL_R2EFF)
+ spin_index = 0
+ for spin, spin_id in spin_loop(return_id=True):
+ # Printout.
+ print("\nSpin %s." % spin_id)
+
+ # Check the fitted parameters.
+ for i in range(len(keys)):
+ self.assertAlmostEqual(spin.r2eff[keys[i]]/10.0,
rates[spin_index][i]/10.0, 2)
+
+ # Increment the spin index.
+ spin_index += 1
+
+ # Switch to the 'M61 skew' model data pipe, then check for each spin.
+ self.interpreter.pipe.switch(MODEL_M61B)
+ spin_index = 0
+ for spin, spin_id in spin_loop(return_id=True):
+ # Printout.
+ print("\nSpin %s." % spin_id)
+
+ # Check the fitted parameters.
+ self.assertAlmostEqual(spin.r2[0]/10,
r1rho_prime[spin_index]/10, 2)
+ self.assertAlmostEqual(spin.pA, pA, 2)
+ self.assertAlmostEqual(spin.dw, dw[spin_index], 2)
+ self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 2)
+
+ # Increment the spin index.
+ spin_index += 1
Copied:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61b.py
(from r19979,
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61b.py?p2=branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61b.py&p1=branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py&r1=19979&r2=19985&rev=19985&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61b.py
Sun Jun 9 10:52:44 2013
@@ -14,7 +14,7 @@
#####################
# The dispersion models.
-MODELS = ['R2eff', 'No Rex', 'M61']
+MODELS = ['R2eff', 'No Rex', 'M61 skew']
# The grid search size (the number of increments per dimension).
GRID_INC = 3
@@ -22,9 +22,6 @@
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
MC_NUM = 3
-# Fixed relaxation time period flag.
-if not hasattr(ds, 'fixed'):
- ds.fixed = True
# Set up the data pipe.
@@ -40,7 +37,7 @@
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+'r1rho_on_res_m61'
+data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_on_res_m61b'
# Create the sequence data.
spin.create(res_name='Trp', res_num=1, spin_name='N')
@@ -50,35 +47,24 @@
spin.isotope(isotope='15N')
# Set the relaxation dispersion experiment type.
-if ds.fixed:
- relax_disp.exp_type('r1rho fixed')
-else:
- relax_disp.exp_type('r1rho exponential')
+relax_disp.exp_type('r1rho fixed')
# The spectral data - spectrum ID, peak lists, offset frequency (Hz),
relaxation time period (s), baseplane RMSD estimate.
data = []
-times = [0.00, 0.01, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12, 0.15]
-ncyc = [1, 2, 3, 4, 5, 6, 7, 8, 9]
-if ds.fixed:
- times = [0.15]
- ncyc = [9]
spin_lock = [1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500,
6000]
for spin_lock_index in range(len(spin_lock)):
- for time_index in range(len(times)):
- data.append(["nu_%s_ncyc%s" % (spin_lock[spin_lock_index],
ncyc[time_index]), "nu_%s_ncyc%s.list" % (spin_lock[spin_lock_index],
ncyc[time_index]), spin_lock[spin_lock_index], times[time_index], 200000.0])
+ data.append(["nu_%s_time_0.1" % spin_lock[spin_lock_index],
"nu_%s_time_0.1.list" % spin_lock[spin_lock_index],
spin_lock[spin_lock_index], 0.1, 200000.0])
# Load the reference spectrum.
-if ds.fixed:
- # Load the peak intensities and set the errors.
- spectrum.read_intensities(file="nu_%s_ncyc1.list" % spin_lock[0],
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='N',
proton='HN')
- spectrum.read_intensities(file="nu_%s_ncyc1.list" % spin_lock[0],
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='NE1',
proton='HE1')
- spectrum.baseplane_rmsd(spectrum_id='ref', error=data[0][4])
+spectrum.read_intensities(file="nu_%s_ref.list" % spin_lock[0],
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='N',
proton='HN')
+spectrum.read_intensities(file="nu_%s_ref.list" % spin_lock[0],
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='NE1',
proton='HE1')
+spectrum.baseplane_rmsd(spectrum_id='ref', error=data[0][4])
- # Set as the reference.
- relax_disp.spin_lock_field(spectrum_id='ref', field=None)
+# Set as the reference.
+relax_disp.spin_lock_field(spectrum_id='ref', field=None)
- # Set the spectrometer frequency.
- spectrometer.frequency(id='ref', frq=800, units='MHz')
+# Set the spectrometer frequency.
+spectrometer.frequency(id='ref', frq=800, units='MHz')
# Loop over the spectral data, loading it and setting the metadata.
for i in range(len(data)):
r19985 - in /branches/relax_disp/test_suite/system_tests: relax_disp.py scripts/relax_disp/r1rho_on_res_m61b.py