Hi Troels, Is the text file checking temporarily commented out in this test?
Cheers, Edward On 30 July 2014 23:43, <[email protected]> wrote: > 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. > > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
