Author: bugman
Date: Mon Sep 9 18:30:53 2013
New Revision: 20936
URL: http://svn.gna.org/viewcvs/relax?rev=20936&view=rev
Log:
Modified system test after inclusion of 1M GuHCl dataset.
Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of
Tollinger/Kay dispersion model (2001)
Following the guide at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_
gmail_dot_com
Signed-off-by: Edward d'Auvergne <edward@xxxxxxxxxxxxx>
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=20936&r1=20935&r2=20936&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Mon Sep 9
18:30:53 2013
@@ -114,7 +114,7 @@
self.interpreter.value.copy(pipe_from='R2eff', pipe_to=model,
param='r2eff')
- def setup_kteilum_fmpoulsen_makke_cpmg_data(self, model=None):
+ def setup_kteilum_fmpoulsen_makke_cpmg_data(self, model=None,
expfolder=None):
"""Set up the data for the
test_kteilum_fmpoulsen_makke_cpmg_data_*() system tests.
@keyword model: The name of the model which will be tested.
@@ -122,7 +122,7 @@
"""
# Create the data pipe and load the base data.
- data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+expfolder
self.interpreter.pipe.create(pipe_name='base pipe',
pipe_type='relax_disp')
self.interpreter.results.read(data_path+sep+'ini_setup_trunc')
@@ -977,14 +977,14 @@
self.assertEqual(spin2[i], lines[i])
- def test_kteilum_fmpoulsen_makke_cpmg_data_to_cr72(self):
+ def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72(self):
"""Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke
2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.
- This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period.
+ This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride).
"""
# Base data setup.
- self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='CR72')
+ self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='CR72',
expfolder="acbp_cpmg_disp_048MGuHCl_40C_041223")
# Alias the spins.
res61L = cdp.mol[0].res[0].spin[0]
@@ -1015,14 +1015,14 @@
self.assertAlmostEqual(res61L.chi2, 65.99987828889657, 5)
- def test_kteilum_fmpoulsen_makke_cpmg_data_to_cr72_full(self):
+ def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72_full(self):
"""Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke
2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.
- This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period.
+ This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride).
"""
# Base data setup.
- self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='CR72 full')
+ self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='CR72 full',
expfolder="acbp_cpmg_disp_048MGuHCl_40C_041223")
# Alias the spins.
res61L = cdp.mol[0].res[0].spin[0]
@@ -1056,12 +1056,57 @@
self.assertAlmostEqual(res61L.chi2, 65.99987828890289, 5)
- def test_kteilum_fmpoulsen_makke_cpmg_data_to_tsmfk01(self):
+ def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_tsmfk01(self):
"""Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke
2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.
- This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period.
-
- The comparison is to Figure 2. This dataset is the 0.48 M GuHCl,
but similar results are expected. The reported results are expected to be in
rad.s^-1. Conversion into relax stored values is preferably.
+ This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride).
+
+ Figure 3 shows the ln( k_a [s^-1]) for different concentrations of
GuHCl. The precise values are:
+
+ - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
+ - 0.483 0.89623903 2.4503699912708878
+ - 0.545 1.1694838
+ - 0.545 1.1761503
+ - 0.622 1.294
+ - 0.669 1.5176493
+ - 0.722 1.6238791
+ - 0.813 1.9395758
+ - 1.011 2.3558415 10.547000429321157
+ """
+
+ # Base data setup.
+ self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='TSMFK01',
expfolder="acbp_cpmg_disp_048MGuHCl_40C_041223")
+
+ # Alias the spins.
+ res61L = cdp.mol[0].res[0].spin[0]
+
+ # Set the initial parameter values.
+ res61L.r2a = [8]
+ res61L.dw = 6.5
+ res61L.k_AB = 2.5
+
+ # Low precision optimisation.
+ self.interpreter.minimise(min_algor='simplex', line_search=None,
hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None,
max_iter=1000, constraints=True, scaling=True, verbosity=1)
+
+ # Printout.
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s" % ("Parameter", "Value (:61)"))
+ print("%-20s %20.15g" % ("R2A (600 MHz)", res61L.r2a[0]))
+ print("%-20s %20.15g" % ("dw", res61L.dw))
+ print("%-20s %20.15g" % ("k_AB", res61L.k_AB))
+ print("%-20s %20.15g\n" % ("chi2", res61L.chi2))
+
+ # Checks for residue :61. Reference values from paper
+
+ self.assertAlmostEqual(res61L.k_AB, 2.45, 1)
+
+
+ def test_kteilum_fmpoulsen_makke_cpmg_data_101m_guhcl_to_tsmfk01(self):
+ """Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke
2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.
+
+ This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period. Experiment in 1.01 M GuHCl (guanidine hydrochloride).
+
+ The comparison is to Figure 2, which is for dataset with 1 M GuHCl.
The reported results are expected to be in rad.s^-1. Conversion into relax
stored values is preferably.
{Representative 15N CPMG relaxation dispersion curve measured on the
cross peaks from residue L61 in folded ACBP at pH 5.3, 1 M GuHCl, and 40C.}
1. The dotted line represents a residue-specific fit of all
parameters in Eq. 1.
@@ -1069,16 +1114,28 @@
- dw = (2.45 +/- 0.09) * 10^3 s^{-1}
- R2 = 8.0 +/- 0.5 s^{-1}.
2. The solid line represents a global fit of k_AB to all protein
residues and a residue-specific fit of dw and R2.}
- -.k_AB = 10.55 +/- 0.08 s^{-1}
+ - k_AB = 10.55 +/- 0.08 s^{-1}
- dw = (2.44 +/- 0.08) * 10^3 s^{-1}
- R2 = 8.4 +/- 0.3 s^{-1}.
Conversion of paper results to relax results is performed by
- dw(ppm) = dw(rad.s^-1) * 10^6 * 1/(2*pi) *
(gyro1H/(gyro15N*spectrometer_freq)) = 2.45E3 * 1E6 / (2 * math.pi) *
(26.7522212E7/(-2.7126E7 * 599.8908622E6)) = -6.41 ppm.
+
+ Figure 3 shows the ln( k_a [s^-1]) for different concentrations of
GuHCl. The precise values are:
+
+ - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
+ - 0.483 0.89623903 2.4503699912708878
+ - 0.545 1.1694838
+ - 0.545 1.1761503
+ - 0.622 1.294
+ - 0.669 1.5176493
+ - 0.722 1.6238791
+ - 0.813 1.9395758
+ - 1.011 2.3558415 10.547000429321157
"""
# Base data setup.
- self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='TSMFK01')
+ self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='TSMFK01',
expfolder="acbp_cpmg_disp_101MGuHCl_40C_041223")
# Alias the spins.
res61L = cdp.mol[0].res[0].spin[0]
@@ -1101,10 +1158,9 @@
# Checks for residue :61. Reference values from paper
- self.assertAlmostEqual(res61L.r2a[0], 8.4, -1)
- self.assertAlmostEqual(res61L.dw, 6.41, 2)
+ self.assertAlmostEqual(res61L.r2a[0], 8.4, 0)
+ self.assertAlmostEqual(res61L.dw, 6.41, 0)
self.assertAlmostEqual(res61L.k_AB, 10.55, 0)
- self.assertAlmostEqual(res61L.chi2, 60.0, 5)
def test_m61_data_to_m61(self):
r20936 - /branches/relax_disp/test_suite/system_tests/relax_disp.py