Hi Edward. I added the systemtest, but I am about to delete it again.
I am not sure how to handle "offset" data for CPMG experiments. I am thinking that I will rather test in specific_analyses/relax_disp/data.py plot_disp_curves() to see if it is a CPMG model, raise a warning, and pass out of the function without doing anything. What do you think? Best Troels 2014-07-31 9:43 GMT+02:00 Edward d'Auvergne <[email protected]>: > 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 _______________________________________________ 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
