The error should now be gone with both of these: http://thread.gmane.org/gmane.science.nmr.relax.scm/19695
Regards, Edward On 10 December 2013 12:05, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > I can say so much, that the error is related to definition of > times = [0.00, 0.01, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12, 0.15] > if one changes it to: > times = [0.15] > > the error vanishes. > > > 2013/12/10 Edward d'Auvergne <[email protected]> >> >> We should then definitely have this tested in the test suite! I just >> had a look at it and will commit the fix very soon. The problem is >> that I have recently introduced the spin-lock (or hard pulse for the >> CPMG) offset dimension into all of the dispersion data structures used >> in the target functions. But the grid_search_setup() method was not >> updated correctly for this. Note the loop_exp_frq_point() function >> call, the fix is to replace it with loop_exp_frq_offset_point() to >> loop over all of these! >> >> Cheers, >> >> Edward >> >> >> >> On 10 December 2013 11:43, Troels Emtekær Linnet <[email protected]> >> wrote: >> > Hi Edward. >> > >> > I can say that running this: >> > relax ./test_suite/shared_data/dispersion/r1rho_on_res_m61/r2eff_calc.py >> > >> > Give the same error. >> > File "/Users/tlinnet/software/relax_trunk/pipe_control/minimise.py", >> > line >> > 152, in grid_search >> > grid_search(lower=lower, upper=upper, inc=inc, >> > constraints=constraints, >> > verbosity=verbosity) >> > File >> > >> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py", >> > line 1093, in grid_search >> > self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, >> > constraints=constraints, verbosity=verbosity, sim_index=sim_index) >> > File >> > >> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py", >> > line 1142, in minimise >> > self._minimise_r2eff(min_algor=min_algor, min_options=min_options, >> > func_tol=func_tol, grad_tol=grad_tol, max_iterations=max_iterations, >> > constraints=constraints, scaling=scaling, verbosity=verbosity, >> > sim_index=sim_index, lower=lower, upper=upper, inc=inc) >> > File >> > >> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py", >> > line 357, in _minimise_r2eff >> > grid_size, inc_new, lower_new, upper_new = >> > grid_search_setup(spins=[spin], spin_ids=[spin_id], >> > param_vector=param_vector, lower=lower, upper=upper, inc=inc, >> > scaling_matrix=scaling_matrix) >> > File >> > >> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/optimisation.py", >> > line 282, in grid_search_setup >> > lower_new.append(lower[i] / scaling_matrix[i, i]) >> > IndexError: list index out of range >> > >> > >> > >> > >> > 2013/12/10 Edward d'Auvergne <[email protected]> >> >> >> >> Hi, >> >> >> >> I saw that, but I'm not sure why it is saying that. Maybe you should >> >> add some debugging printouts in the grid_search_setup() function and >> >> see what is happening? It won't be because of the missing R1 data. I >> >> would suggest that if you would like to develop the code for >> >> optimising R1 as a parameter of the R1rho models (i.e. all of them), >> >> that we should create a special branch for that. I know exactly what >> >> needs to be done and I can direct you in the right direction. But it >> >> needs to be developed in a branch as it will be quite disruptive. >> >> >> >> Regards, >> >> >> >> Edward >> >> >> >> >> >> >> >> On 10 December 2013 09:56, Troels Emtekær Linnet >> >> <[email protected]> >> >> wrote: >> >> > Hi Edward. >> >> > >> >> > I now receive this error: >> >> > relax -s Relax_disp.test_r1rho_kjaergaard >> >> > >> >> > But I guess this is expected, since I do not load any R1 data in. ? >> >> > >> >> > Best >> >> > Troels >> >> > --------- >> >> > relax> relax_disp.select_model(model='R2eff') >> >> > R2eff/R1rho value and error determination. >> >> > >> >> > >> >> > Optimisation >> >> > ============ >> >> > >> >> > >> >> > Nesting and model equivalence checks >> >> > ------------------------------------ >> >> > >> >> > No model nesting or model equivalence detected. >> >> > >> >> > relax> grid_search(lower=None, upper=None, inc=4, constraints=True, >> >> > verbosity=1) >> >> > Traceback (most recent call last): >> >> > File >> >> > >> >> > >> >> > "/Users/tlinnet/software/relax_trunk/test_suite/system_tests/relax_disp.py", >> >> > line 2591, in test_r1rho_kjaergaard >> >> > relax_disp.Relax_disp(pipe_name=pipe_name, >> >> > pipe_bundle=pipe_bundle, >> >> > results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, >> >> > mc_sim_num=MC_NUM, >> >> > modsel=MODSEL) >> >> > File >> >> > "/Users/tlinnet/software/relax_trunk/auto_analyses/relax_disp.py", >> >> > line 116, in __init__ >> >> > self.run() >> >> > File >> >> > "/Users/tlinnet/software/relax_trunk/auto_analyses/relax_disp.py", >> >> > line 451, in run >> >> > self.optimise(model=model) >> >> > File >> >> > "/Users/tlinnet/software/relax_trunk/auto_analyses/relax_disp.py", >> >> > line 350, in optimise >> >> > self.interpreter.grid_search(inc=self.grid_inc) >> >> > File "/Users/tlinnet/software/relax_trunk/prompt/uf_objects.py", >> >> > line >> >> > 221, >> >> > in __call__ >> >> > self._backend(*new_args, **uf_kargs) >> >> > File >> >> > "/Users/tlinnet/software/relax_trunk/pipe_control/minimise.py", >> >> > line >> >> > 152, in grid_search >> >> > grid_search(lower=lower, upper=upper, inc=inc, >> >> > constraints=constraints, >> >> > verbosity=verbosity) >> >> > File >> >> > >> >> > >> >> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py", >> >> > line 1093, in grid_search >> >> > self.minimise(min_algor='grid', lower=lower, upper=upper, >> >> > inc=inc, >> >> > constraints=constraints, verbosity=verbosity, sim_index=sim_index) >> >> > File >> >> > >> >> > >> >> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py", >> >> > line 1142, in minimise >> >> > self._minimise_r2eff(min_algor=min_algor, >> >> > min_options=min_options, >> >> > func_tol=func_tol, grad_tol=grad_tol, max_iterations=max_iterations, >> >> > constraints=constraints, scaling=scaling, verbosity=verbosity, >> >> > sim_index=sim_index, lower=lower, upper=upper, inc=inc) >> >> > File >> >> > >> >> > >> >> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py", >> >> > line 357, in _minimise_r2eff >> >> > grid_size, inc_new, lower_new, upper_new = >> >> > grid_search_setup(spins=[spin], spin_ids=[spin_id], >> >> > param_vector=param_vector, lower=lower, upper=upper, inc=inc, >> >> > scaling_matrix=scaling_matrix) >> >> > File >> >> > >> >> > >> >> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/optimisation.py", >> >> > line 282, in grid_search_setup >> >> > lower_new.append(lower[i] / scaling_matrix[i, i]) >> >> > IndexError: list index out of range >> >> > >> >> > >> >> > 2013/12/10 Edward d'Auvergne <[email protected]> >> >> >> >> >> >> Ah, ok, that would explain the strangeness. Then the simple >> >> >> solution >> >> >> would be to check that the correct data pipe type is being used at >> >> >> the >> >> >> start of both these user functions! Then a user should never reach >> >> >> this failure point. >> >> >> >> >> >> Regards, >> >> >> >> >> >> Edward >> >> >> >> >> >> >> >> >> On 10 December 2013 09:34, Troels Emtekær Linnet >> >> >> <[email protected]> >> >> >> wrote: >> >> >> > Uf... >> >> >> > >> >> >> > There was the error: >> >> >> > >> >> >> > # Set the relaxation times (in s). >> >> >> > >> >> >> > self.interpreter.relax_fit.relax_time(time=time_sl, >> >> >> > spectrum_id=sp_id) >> >> >> > was used instead of: >> >> >> > # Set the relaxation times (in s). >> >> >> > >> >> >> > self.interpreter.relax_disp.relax_time(spectrum_id=sp_id, >> >> >> > time=time_sl) >> >> >> > >> >> >> > >> >> >> > 2013/12/10 Edward d'Auvergne <[email protected]> >> >> >> >> >> >> >> >> Hi, >> >> >> >> >> >> >> >> That's exactly the point of failure. Maybe it would be useful to >> >> >> >> create one or two simple unit tests for the get_curve_type() >> >> >> >> function, >> >> >> >> using some of the data in the current data pipe where your script >> >> >> >> is >> >> >> >> failing. The problem is that for the experiment ID being sent >> >> >> >> into >> >> >> >> it, it can only find one matching relaxation time. Are you sure >> >> >> >> that >> >> >> >> all data is loaded correctly? >> >> >> >> >> >> >> >> Regards, >> >> >> >> >> >> >> >> Edward >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On 10 December 2013 09:19, Troels Emtekær Linnet >> >> >> >> <[email protected]> >> >> >> >> wrote: >> >> >> >> > Hi Edward. >> >> >> >> > >> >> >> >> > The function: has_exponential_exp_type() is returning >> >> >> >> > False, as the get_curve_type(id) is returning: fixed time >> >> >> >> > >> >> >> >> > So that test look good enough for me? >> >> >> >> > >> >> >> >> > Is it the: fixed time which is a problem? >> >> >> >> > >> >> >> >> > Best >> >> >> >> > Troels >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > 2013/12/10 Troels Emtekær Linnet <[email protected]> >> >> >> >> >> >> >> >> >> >> Hi Edward. >> >> >> >> >> >> >> >> >> >> I will try to look into it today. >> >> >> >> >> >> >> >> >> >> Best >> >> >> >> >> Troels >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2013/12/9 Edward d'Auvergne <[email protected]> >> >> >> >> >>> >> >> >> >> >>> Hi Troels, >> >> >> >> >>> >> >> >> >> >>> Note that I will soon release relax 3.1.1 with all of the >> >> >> >> >>> recent >> >> >> >> >>> fixes >> >> >> >> >>> (possibly tomorrow). This includes the 'NS MMQ 3-site', 'NS >> >> >> >> >>> MMQ >> >> >> >> >>> 3-site linear', 'NS R1rho 3-site', and 'NS R1rho 3-site >> >> >> >> >>> linear' >> >> >> >> >>> dispersion models which are now implemented, tested, and find >> >> >> >> >>> similar >> >> >> >> >>> results to Dmitry Korzhnev's cpmg_fit software. If the test >> >> >> >> >>> is >> >> >> >> >>> not >> >> >> >> >>> functional by then, I will disable it for the release. It >> >> >> >> >>> would >> >> >> >> >>> be >> >> >> >> >>> very useful to have fixed though as it looks like variable >> >> >> >> >>> relaxation >> >> >> >> >>> time data (SQ CPMG, MMQ CPMG, or R1rho) will all currently >> >> >> >> >>> fail >> >> >> >> >>> in >> >> >> >> >>> the >> >> >> >> >>> auto-analysis. I've had a look and have another hint for you >> >> >> >> >>> - >> >> >> >> >>> the >> >> >> >> >>> problem is that has_exponential_exp_type() function is not >> >> >> >> >>> returning >> >> >> >> >>> the correct answer ;) >> >> >> >> >>> >> >> >> >> >>> Regards, >> >> >> >> >>> >> >> >> >> >>> Edward >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> On 9 December 2013 18:12, Edward d'Auvergne >> >> >> >> >>> <[email protected]> >> >> >> >> >>> wrote: >> >> >> >> >>> > Hi, >> >> >> >> >>> > >> >> >> >> >>> > This is a strange failure! The auto-analysis should not be >> >> >> >> >>> > running >> >> >> >> >>> > the calc user function for this. That is the problem, you >> >> >> >> >>> > cannot >> >> >> >> >>> > run >> >> >> >> >>> > the calc user function for non-constant relaxation time >> >> >> >> >>> > experiments. >> >> >> >> >>> > The error message is the standard one to tell the user >> >> >> >> >>> > that. >> >> >> >> >>> > The >> >> >> >> >>> > grid_search and minimise user functions should be used >> >> >> >> >>> > instead >> >> >> >> >>> > (maybe >> >> >> >> >>> > the error message can be modified to clarify this and >> >> >> >> >>> > include >> >> >> >> >>> > this >> >> >> >> >>> > info). But it is the auto-analysis that is running this. >> >> >> >> >>> > So >> >> >> >> >>> > the >> >> >> >> >>> > problem is there. relax can of course handle variable >> >> >> >> >>> > relaxation >> >> >> >> >>> > times for any dispersion data type. >> >> >> >> >>> > >> >> >> >> >>> > Regards, >> >> >> >> >>> > >> >> >> >> >>> > Edward >> >> >> >> >>> > >> >> >> >> >>> > >> >> >> >> >>> > >> >> >> >> >>> > >> >> >> >> >>> > On 9 December 2013 18:02, Troels Emtekær Linnet >> >> >> >> >>> > <[email protected]> >> >> >> >> >>> > wrote: >> >> >> >> >>> >> Hi Edward. >> >> >> >> >>> >> >> >> >> >> >>> >> The R1rho data is not constant time. >> >> >> >> >>> >> >> >> >> >> >>> >> I have only included the models: >> >> >> >> >>> >> MODELS = ['R2eff', 'No Rex', 'DPL94'] >> >> >> >> >>> >> >> >> >> >> >>> >> I have set it up, to find a solution for analysing R1rho >> >> >> >> >>> >> data, >> >> >> >> >>> >> where >> >> >> >> >>> >> R1 data >> >> >> >> >>> >> has not been acquired, but for >> >> >> >> >>> >> different >> >> >> >> >>> >> >> >> >> >> >>> >> It actually also fails at the moment, and will probably do >> >> >> >> >>> >> for >> >> >> >> >>> >> some >> >> >> >> >>> >> time. >> >> >> >> >>> >> >> >> >> >> >>> >> -------- >> >> >> >> >>> >> relax -s Relax_disp.test_r1rho_kjaergaar >> >> >> >> >>> >> >> >> >> >> >>> >> relax> calc(verbosity=1) >> >> >> >> >>> >> Traceback (most recent call last): >> >> >> >> >>> >> File >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/relax_disp.py", >> >> >> >> >>> >> line 2581, in test_r1rho_kjaergaard >> >> >> >> >>> >> relax_disp.Relax_disp(pipe_name=pipe_name, >> >> >> >> >>> >> pipe_bundle=pipe_bundle, >> >> >> >> >>> >> results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, >> >> >> >> >>> >> mc_sim_num=MC_NUM, >> >> >> >> >>> >> modsel=MODSEL) >> >> >> >> >>> >> File >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py", >> >> >> >> >>> >> line 116, in __init__ >> >> >> >> >>> >> self.run() >> >> >> >> >>> >> File >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py", >> >> >> >> >>> >> line 447, in run >> >> >> >> >>> >> self.interpreter.calc() >> >> >> >> >>> >> File >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/uf_objects.py", >> >> >> >> >>> >> line 221, in __call__ >> >> >> >> >>> >> self._backend(*new_args, **uf_kargs) >> >> >> >> >>> >> File >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/pipe_control/minimise.py", >> >> >> >> >>> >> line 86, in calc >> >> >> >> >>> >> calculate(verbosity=verbosity) >> >> >> >> >>> >> File >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py", >> >> >> >> >>> >> line 717, in calculate >> >> >> >> >>> >> self._calculate_r2eff() >> >> >> >> >>> >> File >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py", >> >> >> >> >>> >> line 182, in _calculate_r2eff >> >> >> >> >>> >> check_exp_type_fixed_time() >> >> >> >> >>> >> File >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/checks.py", >> >> >> >> >>> >> line 112, in check_exp_type_fixed_time >> >> >> >> >>> >> raise RelaxError("The experiment '%s' is not of the >> >> >> >> >>> >> fixed >> >> >> >> >>> >> relaxation >> >> >> >> >>> >> time period data type." % exp_type) >> >> >> >> >>> >> RelaxError: RelaxError: The experiment 'R1rho' is not of >> >> >> >> >>> >> the >> >> >> >> >>> >> fixed >> >> >> >> >>> >> relaxation time period data type. >> >> >> >> >>> >> >> >> >> >> >>> >> -------------- >> >> >> >> >>> >> >> >> >> >> >>> >> Is the R1rho analysis only implemented for fixed time >> >> >> >> >>> >> periods? >> >> >> >> >>> >> >> >> >> >> >>> >> Best >> >> >> >> >>> >> Troels >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> 2013/12/9 Edward d'Auvergne <[email protected]> >> >> >> >> >>> >>> >> >> >> >> >>> >>> Hi Troels, >> >> >> >> >>> >>> >> >> >> >> >>> >>> When looking at this data and analysis, remember that I >> >> >> >> >>> >>> have >> >> >> >> >>> >>> not >> >> >> >> >>> >>> implemented Dmitry Korzhnev's "correction" for constant >> >> >> >> >>> >>> time >> >> >> >> >>> >>> R1rho >> >> >> >> >>> >>> data. I don't know if that was used in the original >> >> >> >> >>> >>> publication >> >> >> >> >>> >>> for >> >> >> >> >>> >>> your data. More details are given in the 'To do' section >> >> >> >> >>> >>> of >> >> >> >> >>> >>> the >> >> >> >> >>> >>> manual (I only recently added this info). I also don't >> >> >> >> >>> >>> know >> >> >> >> >>> >>> what >> >> >> >> >>> >>> the >> >> >> >> >>> >>> rest of the field think of his correction and how it >> >> >> >> >>> >>> applies >> >> >> >> >>> >>> to >> >> >> >> >>> >>> later >> >> >> >> >>> >>> models from the Palmer group. >> >> >> >> >>> >>> >> >> >> >> >>> >>> Regards, >> >> >> >> >>> >>> >> >> >> >> >>> >>> Edward >> >> >> >> >>> >>> >> >> >> >> >>> >>> >> >> >> >> >>> >>> >> >> >> >> >>> >>> On 9 December 2013 17:49, <[email protected]> wrote: >> >> >> >> >>> >>> > Author: tlinnet >> >> >> >> >>> >>> > Date: Mon Dec 9 17:49:49 2013 >> >> >> >> >>> >>> > New Revision: 21920 >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > URL: >> >> >> >> >>> >>> > http://svn.gna.org/viewcvs/relax?rev=21920&view=rev >> >> >> >> >>> >>> > Log: >> >> >> >> >>> >>> > Added system test for the analysis of optimisation of >> >> >> >> >>> >>> > the >> >> >> >> >>> >>> > Kjaergaard et >> >> >> >> >>> >>> > al., 2013 Off-resonance R1rho relaxation dispersion >> >> >> >> >>> >>> > experiments >> >> >> >> >>> >>> > using the >> >> >> >> >>> >>> > 'DPL' model. >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > Work in progress for Support Request #3083, >> >> >> >> >>> >>> > (https://gna.org/support/index.php?3083) - Addition of >> >> >> >> >>> >>> > Data-set >> >> >> >> >>> >>> > for R1rho >> >> >> >> >>> >>> > analysis. >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > Modified: >> >> >> >> >>> >>> > trunk/test_suite/system_tests/relax_disp.py >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > Modified: trunk/test_suite/system_tests/relax_disp.py >> >> >> >> >>> >>> > URL: >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21920&r1=21919&r2=21920&view=diff >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > ============================================================================== >> >> >> >> >>> >>> > --- trunk/test_suite/system_tests/relax_disp.py >> >> >> >> >>> >>> > (original) >> >> >> >> >>> >>> > +++ trunk/test_suite/system_tests/relax_disp.py Mon Dec >> >> >> >> >>> >>> > 9 >> >> >> >> >>> >>> > 17:49:49 >> >> >> >> >>> >>> > 2013 >> >> >> >> >>> >>> > @@ -2450,6 +2450,137 @@ >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, >> >> >> >> >>> >>> > 0.030959849811015544, 3) >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > + def test_r1rho_kjaergaard(self): >> >> >> >> >>> >>> > + """Optimisation of the Kjaergaard et al., 2013 >> >> >> >> >>> >>> > Off-resonance >> >> >> >> >>> >>> > R1rho relaxation dispersion experiments using the 'DPL' >> >> >> >> >>> >>> > model. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + This uses the data from Kjaergaard's paper at >> >> >> >> >>> >>> > U{DOI: >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + """ >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # The path to the data files. >> >> >> >> >>> >>> > + data_path = status.install_path + >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Set pipe name, bundle and type. >> >> >> >> >>> >>> > + pipe_name = 'base pipe' >> >> >> >> >>> >>> > + pipe_bundle = 'relax_disp' >> >> >> >> >>> >>> > + pipe_type= 'relax_disp' >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Create the data pipe. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > self.interpreter.pipe.create(pipe_name=pipe_name, >> >> >> >> >>> >>> > bundle=pipe_bundle, pipe_type=pipe_type) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Read the spins. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > self.interpreter.spectrum.read_spins(file='1_0_46_0_max_standard.ser', >> >> >> >> >>> >>> > dir=data_path+sep+'peak_lists') >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Test some of the sequence. >> >> >> >> >>> >>> > + self.assertEqual(len(cdp.mol), 1) >> >> >> >> >>> >>> > + self.assertEqual(cdp.mol[0].name, None) >> >> >> >> >>> >>> > + self.assertEqual(len(cdp.mol[0].res), 48) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Name the isotope for field strength scaling. >> >> >> >> >>> >>> > + self.interpreter.spin.isotope(isotope='15N') >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Set number of experiments to be used. >> >> >> >> >>> >>> > + NR_exp = -1 >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Load the experiments settings file. >> >> >> >> >>> >>> > + expfile = >> >> >> >> >>> >>> > open(data_path+sep+'exp_parameters_sort.txt','r') >> >> >> >> >>> >>> > + expfileslines = expfile.readlines()[:NR_exp] >> >> >> >> >>> >>> > + expfile.close() >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # In MHz >> >> >> >> >>> >>> > + yOBS = 81.050 >> >> >> >> >>> >>> > + # In ppm >> >> >> >> >>> >>> > + yCAR = 118.078 >> >> >> >> >>> >>> > + centerPPM_N15 = yCAR >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + ## Read the chemical shift data. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > self.interpreter.chemical_shift.read(file='1_0_46_0_max_standard.ser', >> >> >> >> >>> >>> > dir=data_path+sep+'peak_lists') >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Test the chemical shift data. >> >> >> >> >>> >>> > + cs = [122.223, 122.162, 114.250, 125.852, >> >> >> >> >>> >>> > 118.626, >> >> >> >> >>> >>> > 117.449, >> >> >> >> >>> >>> > 119.999, 122.610, 118.602, 118.291, 115.393, >> >> >> >> >>> >>> > + 121.288, 117.448, 116.378, 116.316, 117.263, >> >> >> >> >>> >>> > 122.211, >> >> >> >> >>> >>> > 118.748, >> >> >> >> >>> >>> > 118.103, 119.421, 119.317, 119.386, 117.279, >> >> >> >> >>> >>> > + 122.103, 120.038, 116.698, 111.811, 118.639, >> >> >> >> >>> >>> > 118.285, >> >> >> >> >>> >>> > 121.318, >> >> >> >> >>> >>> > 117.770, 119.948, 119.759, 118.314, 118.160, >> >> >> >> >>> >>> > + 121.442, 118.714, 113.080, 125.706, 119.183, >> >> >> >> >>> >>> > 120.966, >> >> >> >> >>> >>> > 122.361, >> >> >> >> >>> >>> > 126.675, 117.069, 120.875, 109.372, 119.811, 126.048] >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + i = 0 >> >> >> >> >>> >>> > + for spin, spin_id in >> >> >> >> >>> >>> > spin_loop(return_id=True): >> >> >> >> >>> >>> > + print spin.name, spin.num, spin_id, >> >> >> >> >>> >>> > spin.chemical_shift, >> >> >> >> >>> >>> > cs[i] >> >> >> >> >>> >>> > + # Check the chemical shift. >> >> >> >> >>> >>> > + self.assertEqual(spin.chemical_shift, >> >> >> >> >>> >>> > cs[i]) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Increment the index. >> >> >> >> >>> >>> > + i += 1 >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # The lock power to field, has been found in >> >> >> >> >>> >>> > an >> >> >> >> >>> >>> > calibration >> >> >> >> >>> >>> > experiment. >> >> >> >> >>> >>> > + spin_lock_field_strengths_Hz = {'35': 431.0, >> >> >> >> >>> >>> > '39': >> >> >> >> >>> >>> > 651.2, >> >> >> >> >>> >>> > '41': >> >> >> >> >>> >>> > 800.5, '43': 984.0, '46': 1341.11, '48': 1648.5} >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Apply spectra settings. >> >> >> >> >>> >>> > + for i in range(len(expfileslines)): >> >> >> >> >>> >>> > + line=expfileslines[i] >> >> >> >> >>> >>> > + if line[0] == "#": >> >> >> >> >>> >>> > + continue >> >> >> >> >>> >>> > + else: >> >> >> >> >>> >>> > + # DIRN I deltadof2 dpwr2slock ncyc >> >> >> >> >>> >>> > trim >> >> >> >> >>> >>> > ss >> >> >> >> >>> >>> > sfrq >> >> >> >> >>> >>> > + DIRN = line.split()[0] >> >> >> >> >>> >>> > + I = int(line.split()[1]) >> >> >> >> >>> >>> > + deltadof2 = line.split()[2] >> >> >> >> >>> >>> > + dpwr2slock = line.split()[3] >> >> >> >> >>> >>> > + ncyc = int(line.split()[4]) >> >> >> >> >>> >>> > + trim = float(line.split()[5]) >> >> >> >> >>> >>> > + ss = int(line.split()[6]) >> >> >> >> >>> >>> > + set_sfrq = float(line.split()[7]) >> >> >> >> >>> >>> > + apod_rmsd = float(line.split()[8]) >> >> >> >> >>> >>> > + spin_lock_field_strength = >> >> >> >> >>> >>> > spin_lock_field_strengths_Hz[dpwr2slock] >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Calculate spin_lock time >> >> >> >> >>> >>> > + time_sl = 2*ncyc*trim >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Define file name for peak list. >> >> >> >> >>> >>> > + FNAME = >> >> >> >> >>> >>> > "%s_%s_%s_%s_max_standard.ser"%(I, >> >> >> >> >>> >>> > deltadof2, >> >> >> >> >>> >>> > dpwr2slock, ncyc) >> >> >> >> >>> >>> > + sp_id = "%s_%s_%s_%s"%(I, deltadof2, >> >> >> >> >>> >>> > dpwr2slock, >> >> >> >> >>> >>> > ncyc) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Load the peak intensities. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > self.interpreter.spectrum.read_intensities(file=FNAME, >> >> >> >> >>> >>> > dir=data_path+sep+'peak_lists', spectrum_id=sp_id, >> >> >> >> >>> >>> > int_method='height') >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Set the peak intensity errors, as >> >> >> >> >>> >>> > defined >> >> >> >> >>> >>> > as >> >> >> >> >>> >>> > the >> >> >> >> >>> >>> > baseplane RMSD. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > self.interpreter.spectrum.baseplane_rmsd(error=apod_rmsd, >> >> >> >> >>> >>> > spectrum_id=sp_id) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Set the relaxation dispersion >> >> >> >> >>> >>> > experiment >> >> >> >> >>> >>> > type. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > self.interpreter.relax_disp.exp_type(spectrum_id=sp_id, >> >> >> >> >>> >>> > exp_type='R1rho') >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Set The spin-lock field strength, >> >> >> >> >>> >>> > nu1, >> >> >> >> >>> >>> > in >> >> >> >> >>> >>> > Hz >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > self.interpreter.relax_disp.spin_lock_field(spectrum_id=sp_id, >> >> >> >> >>> >>> > field=spin_lock_field_strength) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Calculating the spin-lock offset in >> >> >> >> >>> >>> > ppm, >> >> >> >> >>> >>> > from >> >> >> >> >>> >>> > offsets >> >> >> >> >>> >>> > values provided in Hz. >> >> >> >> >>> >>> > + frq_N15_Hz = yOBS * 1E6 >> >> >> >> >>> >>> > + offset_ppm_N15 = float(deltadof2) / >> >> >> >> >>> >>> > frq_N15_Hz >> >> >> >> >>> >>> > * >> >> >> >> >>> >>> > 1E6 >> >> >> >> >>> >>> > + omega_rf_ppm = centerPPM_N15 + >> >> >> >> >>> >>> > offset_ppm_N15 >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Set The spin-lock offset, omega_rf, >> >> >> >> >>> >>> > in >> >> >> >> >>> >>> > ppm. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > self.interpreter.relax_disp.spin_lock_offset(spectrum_id=sp_id, >> >> >> >> >>> >>> > offset=omega_rf_ppm) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Set the relaxation times (in s). >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > self.interpreter.relax_fit.relax_time(time=time_sl, >> >> >> >> >>> >>> > spectrum_id=sp_id) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Set the spectrometer frequency. >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > self.interpreter.spectrometer.frequency(id=sp_id, >> >> >> >> >>> >>> > frq=set_sfrq, units='MHz') >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # The dispersion models. >> >> >> >> >>> >>> > + MODELS = ['R2eff', 'No Rex', 'DPL94'] >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # The grid search size (the number of >> >> >> >> >>> >>> > increments >> >> >> >> >>> >>> > per >> >> >> >> >>> >>> > dimension). >> >> >> >> >>> >>> > + GRID_INC = 4 >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # The number of Monte Carlo simulations to be >> >> >> >> >>> >>> > used >> >> >> >> >>> >>> > for >> >> >> >> >>> >>> > error >> >> >> >> >>> >>> > analysis at the end of the analysis. >> >> >> >> >>> >>> > + MC_NUM = 3 >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Model selection technique. >> >> >> >> >>> >>> > + MODSEL = 'AIC' >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + # Run the analysis. >> >> >> >> >>> >>> > + relax_disp.Relax_disp(pipe_name=pipe_name, >> >> >> >> >>> >>> > pipe_bundle=pipe_bundle, results_dir=ds.tmpdir, >> >> >> >> >>> >>> > models=MODELS, >> >> >> >> >>> >>> > grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL) >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > + >> >> >> >> >>> >>> > def test_r2eff_read(self): >> >> >> >> >>> >>> > """Test the operation of the >> >> >> >> >>> >>> > relax_disp.r2eff_read >> >> >> >> >>> >>> > user >> >> >> >> >>> >>> > function.""" >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > >> >> >> >> >>> >>> > _______________________________________________ >> >> >> >> >>> >>> > 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
