Hi, I had noticed that this commit had killed the entire branch ;) That's ok though, because this is a branch and not the trunk. The best fix would be to use the model information. One of the arguments to this param_conversion() function is 'spins'. This is a list of all the spins in the cluster. The key is that every spin container holds the model name for the cluster. There is another part of this module which uses the model information, just search for where the MODEL_M61B variable is used. You should perform a similar test, and only perform the kex to k_AB conversion for the list of models in which this conversion is possible (i.e. they must have a pA and kex parameter).
I have also noticed that the conversion is only half there. There should also be the kex to k_BA conversion as well! Regards, Edward On 11 September 2013 09:47, Troels Emtekær Linnet <[email protected]> wrote: > Dear Edward. > > This commit introduced a fatal bug, making the whole systemtest fail. > > -------- > # The kex to k_AB conversion. > if param_name == 'kex': > # Get pA value. > pA = get_value(key=key, spins=spins, sim_index=sim_index, > param_name='pA', spin_index=spin_index, frq_index=frq_index) > k_AB = value * (1.0 - pA) > set_value(value=k_AB, key=key, spins=spins, > sim_index=sim_index, param_name='k_AB', spin_index=spin_index, > frq_index=frq_index) > ----- > > For example does the LM63 not contain the pA value. > And so it will fail with an AttributeError. > > A not very elegant solution is: > ------------ > # The kex to k_AB conversion. > if param_name == 'kex': > # Try tp get the pA value and set it. > try: > pA = get_value(key=key, spins=spins, > sim_index=sim_index, param_name='pA', spin_index=spin_index, > frq_index=frq_index) > k_AB = value * (1.0 - pA) > set_value(value=k_AB, key=key, spins=spins, > sim_index=sim_index, param_name='k_AB', spin_index=spin_index, > frq_index=frq_index) > except AttributeError: > pass > ------------ > But "try" statements should always be avoided. > > Another possibility is to do a run through the generator: loop_parameters. > First add the available parameters to a list, and then loop over the > generator. > > Then do a check if 'pA' is in the parameter list. > > What do you think? > > Best > Troels Emtekær Linnet > > > > ---------- Forwarded message ---------- > From: <[email protected]> > Date: 2013/9/10 > Subject: r20966 - in /branches/relax_disp: auto_analyses/ > specific_analyses/relax_disp/ test_suite/system_tests/ > To: [email protected] > > > Author: bugman > Date: Tue Sep 10 14:39:51 2013 > New Revision: 20966 > > URL: http://svn.gna.org/viewcvs/relax?rev=20966&view=rev > Log: > Added the conversion to k_AB from kex and pA. k_AB = kex * (1.0 - pA). > > 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 <[email protected]> > > Modified: > branches/relax_disp/auto_analyses/relax_disp.py > branches/relax_disp/specific_analyses/relax_disp/api.py > branches/relax_disp/specific_analyses/relax_disp/parameters.py > branches/relax_disp/test_suite/system_tests/relax_disp.py > > Modified: branches/relax_disp/auto_analyses/relax_disp.py > URL: > http://svn.gna.org/viewcvs/relax/branches/relax_disp/auto_analyses/relax_disp.py?rev=20966&r1=20965&r2=20966&view=diff > ============================================================================== > --- branches/relax_disp/auto_analyses/relax_disp.py (original) > +++ branches/relax_disp/auto_analyses/relax_disp.py Tue Sep 10 14:39:51 2013 > @@ -417,10 +417,12 @@ > self.interpreter.value.write(param='dw', file='dw.out', > dir=path, force=True) > self.interpreter.grace.write(x_data_type='res_num', > y_data_type='dw', file='dw.agr', dir=path, force=True) > > - # The kex and tex parameters. > + # The k_AB, kex and tex parameters. > if model in [None, MODEL_LM63, MODEL_CR72, MODEL_CR72_FULL, > MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, > MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, > MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_2SITE, MODEL_TP02]: > + self.interpreter.value.write(param='k_AB', > file='k_AB.out', dir=path, force=True) > self.interpreter.value.write(param='kex', file='kex.out', > dir=path, force=True) > self.interpreter.value.write(param='tex', file='tex.out', > dir=path, force=True) > + self.interpreter.grace.write(x_data_type='res_num', > y_data_type='k_AB', file='k_AB.agr', dir=path, force=True) > self.interpreter.grace.write(x_data_type='res_num', > y_data_type='kex', file='kex.agr', dir=path, force=True) > self.interpreter.grace.write(x_data_type='res_num', > y_data_type='tex', file='tex.agr', dir=path, force=True) > > > Modified: branches/relax_disp/specific_analyses/relax_disp/api.py > URL: > http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=20966&r1=20965&r2=20966&view=diff > ============================================================================== > --- branches/relax_disp/specific_analyses/relax_disp/api.py (original) > +++ branches/relax_disp/specific_analyses/relax_disp/api.py Tue Sep 10 > 14:39:51 2013 > @@ -1517,6 +1517,9 @@ > pairs['pA'] = 'pB' > pairs['pB'] = 'pA' > > + # Add the names of kex-k_AB pair. > + pairs['k_AB'] = 'kex' > + > # Get the minimisation statistic object names. > min_names = self.data_names(set='min') > > > Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py > URL: > http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=20966&r1=20965&r2=20966&view=diff > ============================================================================== > --- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original) > +++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Tue > Sep 10 14:39:51 2013 > @@ -716,6 +716,13 @@ > tex = 1.0 / (2.0 * value) > set_value(value=tex, key=key, spins=spins, > sim_index=sim_index, param_name='tex', spin_index=spin_index, > frq_index=frq_index) > > + # The kex to k_AB conversion. > + if param_name == 'kex': > + # Get pA value. > + pA = get_value(key=key, spins=spins, sim_index=sim_index, > param_name='pA', spin_index=spin_index, frq_index=frq_index) > + k_AB = value * (1.0 - pA) > + set_value(value=k_AB, key=key, spins=spins, > sim_index=sim_index, param_name='k_AB', spin_index=spin_index, > frq_index=frq_index) > + > # The tex to kex conversion. > if param_name == 'tex': > kex = 1.0 / (2.0 * value) > > 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=20966&r1=20965&r2=20966&view=diff > ============================================================================== > --- branches/relax_disp/test_suite/system_tests/relax_disp.py (original) > +++ branches/relax_disp/test_suite/system_tests/relax_disp.py Tue Sep > 10 14:39:51 2013 > @@ -1014,6 +1014,9 @@ > self.assertAlmostEqual(res61L.kex, 609.262167216419, 0) > self.assertAlmostEqual(res61L.chi2, 65.99987828889657, 5) > > + # Test the conversion to k_AB from kex and pA. > + self.assertEqual(res61L.k_AB, res61L.kex * (1.0 - res61L.pA)) > + > > 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. > > > _______________________________________________ > 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
