Author: tlinnet
Date: Wed Jul 30 23:43:22 2014
New Revision: 24865
URL: http://svn.gna.org/viewcvs/relax?rev=24865&view=rev
Log:
Added systemtest Relax_disp.test_kteilum_fmpoulsen_makke_check_graphs()
to check all possible combinations of dispersion plotting.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
Modified:
branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
Modified: branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/test_suite/system_tests/relax_disp.py?rev=24865&r1=24864&r2=24865&view=diff
==============================================================================
--- branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
(original)
+++ branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
Wed Jul 30 23:43:22 2014
@@ -4108,6 +4108,114 @@
self.assertAlmostEqual(spin.chi2/1000, 162.511988511609/1000, 3)
+ def test_kteilum_fmpoulsen_makke_check_graphs(self):
+ """Check of all possible dispersion graphs from 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 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.
+ model = 'TSMFK01'
+ expfolder = "acbp_cpmg_disp_048MGuHCl_40C_041223"
+ self.setup_kteilum_fmpoulsen_makke_cpmg_data(model=model,
expfolder=expfolder)
+
+ # Alias the spins.
+ res61L = cdp.mol[0].res[0].spin[0]
+
+ # The R20 keys.
+ r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=599.89086220e6)
+
+ # Set the initial parameter values.
+ res61L.r2a = {r20_key1: 8.0}
+ 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)
+
+ # Start testing all possible combinations of graphs.
+ y_axis_types = [Y_AXIS_R2_EFF, Y_AXIS_R2_R1RHO]
+ x_axis_types = [X_AXIS_DISP, X_AXIS_THETA, X_AXIS_W_EFF]
+ interpolate_types = [INTERPOLATE_DISP, INTERPOLATE_OFFSET]
+
+ # Write to temp folder.
+ result_dir_name = ds.tmpdir
+ result_folders = [model]
+ spin_id = ":61@N"
+
+ # Loop through all possible combinations of y_axis, x_axis and
interpolation.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+expfolder+sep+'check_graphs'
+
+ for result_folder in result_folders:
+ # Initial counter per graph, per model.
+ i = 1
+ for y_axis in y_axis_types:
+ for x_axis in x_axis_types:
+ for interpolate in interpolate_types:
+ # Determine file name:
+ file_name_ini =
return_grace_file_name_ini(y_axis=y_axis, x_axis=x_axis,
interpolate=interpolate)
+
+ # Make the file name.
+ file_name = "%s%s.agr" % (file_name_ini,
spin_id.replace('#', '_').replace(':', '_').replace('@', '_'))
+
+ # Set result folder.
+ dir_folder = "%i"%(i)
+
+ # Write the curves.
+ dir =
result_dir_name+sep+result_folder+sep+dir_folder
+ print("Plotting combination of %s, %s,
%s"%(y_axis, x_axis, interpolate))
+
self.interpreter.relax_disp.plot_disp_curves(dir=dir, y_axis=y_axis,
x_axis=x_axis, interpolate=interpolate, force=True)
+
+ # Get the file path.
+ file_path = get_file_path(file_name, dir)
+
+ # Test the plot file exists.
+ print("Testing file access to graph:
%s"%file_path)
+ self.assert_(access(file_path, F_OK))
+
+ # Now open, and compare content, line by line.
+ file_prod = open(file_path)
+ lines_prod = file_prod.readlines()
+ file_prod.close()
+
+ # Define file to compare against.
+ #dir_comp =
data_path+sep+result_folder+sep+dir_folder
+ #file_path_comp = get_file_path(file_name,
dir_comp)
+ #file_comp = open(file_path_comp)
+ #lines_comp = file_comp.readlines()
+ #file_comp.close()
+
+ ## Assert number of lines is equal.
+ #self.assertEqual(len(lines_prod),
len(lines_comp))
+ #for j in range(len(lines_prod)):
+ # # Make the string test
+ # first_char = lines_prod[j][0]
+ # if first_char in ["@", "&"]:
+ # self.assertEqual(lines_prod[j],
lines_comp[j])
+ # else:
+ # # Split string in x, y, error.
+ # # The error would change per run.
+ # x_prod, y_prod, y_prod_err =
lines_prod[j].split()
+ # x_comp, y_comp, y_comp_err =
lines_comp[j].split()
+ # self.assertAlmostEqual(float(x_prod),
float(x_comp))
+ # self.assertAlmostEqual(float(y_prod),
float(y_comp))
+
+ # Add to counter.
+ i += 1
+
+
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.
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Re: r24865 - /branches/r1rho_plotting/test_suite/system_tests/relax_disp.py