Author: bugman Date: Thu Aug 21 14:52:29 2014 New Revision: 25168 URL: http://svn.gna.org/viewcvs/relax?rev=25168&view=rev Log: Removed all references to the 'No Rex R1rho off res' model in the system tests. In addition, the Relax_disp.test_convert_no_rex system test has been deleted as it no longer has a purpose. For the Relax_disp.test_model_nesting_and_param system test, to allow this to work the cdp.exp_type_list list is set to EXP_TYPE_LIST. 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=25168&r1=25167&r2=25168&view=diff ============================================================================== --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Thu Aug 21 14:52:29 2014 @@ -37,8 +37,8 @@ from specific_analyses.relax_disp.checks import check_missing_r1 from specific_analyses.relax_disp.data import generate_r20_key, get_curve_type, has_r1rho_exp_type, loop_exp_frq, loop_exp_frq_offset_point, return_grace_file_name_ini, return_param_key_from_data from specific_analyses.relax_disp.data import INTERPOLATE_DISP, INTERPOLATE_OFFSET, X_AXIS_DISP, X_AXIS_W_EFF, X_AXIS_THETA, Y_AXIS_R2_R1RHO, Y_AXIS_R2_EFF -from specific_analyses.relax_disp.model import convert_no_rex, models_info, nesting_param -from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ, EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC_CPMG, MODEL_LIST_FULL, MODEL_LIST_NUMERIC_CPMG, MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02, MODEL_TAP03 +from specific_analyses.relax_disp.model import models_info, nesting_param +from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ, EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST, EXP_TYPE_R1RHO, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC_CPMG, MODEL_LIST_FULL, MODEL_LIST_NUMERIC_CPMG, MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02, MODEL_TAP03 from status import Status; status = Status() from test_suite.system_tests.base_classes import SystemTestCase @@ -1389,183 +1389,6 @@ # Check R1. check_missing_r1_return = check_missing_r1(model=MODEL_DPL94) self.assertEqual(check_missing_r1_return, False) - - - def test_convert_no_rex(self): - """Test of specific_analyses.relax_disp.model.convert_no_rex() function.""" - - # Set up some spins. - self.setup_missing_r1_spins() - - # Set variables. - exp_type = 'R1rho' - frq = 800.1 * 1E6 - - spectrum_id='test' - - # Set an experiment type to the pipe. - self.interpreter.relax_disp.exp_type(spectrum_id=spectrum_id, exp_type=exp_type) - - # Set a frequency to loop through. - self.interpreter.spectrometer.frequency(id=spectrum_id, frq=frq, units='Hz') - - ##### Test the translations, if R1 is not present. - - # First check that CPMG models are not converted. - - ## First check analytic. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX] + MODEL_LIST_ANALYTIC_CPMG - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, self_models) - - ## First check numeric. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX] + MODEL_LIST_NUMERIC_CPMG - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, self_models) - - # Then check the R1ho models which is available through the GUI. - - ## Check for a normal 2 site setup. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]) - - ## Check for a 2 site setup, where both MODEL_NOREX and MODEL_NOREX_R1RHO are sent to auto_analyses. - ## This should not be possible through the GUI, but could be wished to do through scripting. - ## This should just make a conversion to the 'R1 fit' models, and keep MODEL_NOREX. - - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]) - - ## Check again with MODEL_NOREX_R1RHO. - - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]) - - ## Now check if there is a mix of On-resonance and Off-resonance models. - ## This should insert 'MODEL_NOREX_R1RHO', if it is not present. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_M61, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]) - - ##### Test the translations, if R1 is present. - - ## The path to the data files. - data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' - - ## Now load some R1 data. - self.interpreter.relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) - - # First check that CPMG models are not converted. - - ## First check analytic. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX] + MODEL_LIST_ANALYTIC_CPMG - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, self_models) - - ## First check numeric. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX] + MODEL_LIST_NUMERIC_CPMG - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, self_models) - - # Then check the R1ho models which is available through the GUI. - - ## Check for a normal 2 site setup. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]) - - ## Check for a 2 site setup, including a 3 site. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE_LINEAR] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE_LINEAR]) - - ## Check for a 2 site setup, where both MODEL_NOREX and MODEL_NOREX_R1RHO are sent to auto_analyses. - ## This should not be possible through the GUI, but could be wished to do through scripting. - ## This should just make a conversion to the 'R1 fit' models, and keep MODEL_NOREX. - - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]) - - ## Check again with MODEL_NOREX_R1RHO. - - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]) - - ## Now check if there is a mix of On-resonance and Off-resonance models. - ## This should insert 'MODEL_NOREX_R1RHO', if it is not present. - ### Setup the models, which is available through the GUI. - self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] - - ### Get the return after the conversion. - self_models_return = convert_no_rex(self_models=self_models)[0] - - ### Check that the models have been translated correctly. - self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_M61, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]) def test_cpmg_synthetic_b14_to_ns3d_cluster(self): @@ -5028,6 +4851,9 @@ def test_model_nesting_and_param(self): """Test that all models which can nest, have all their parameters converted.""" + # Set the experiment type. + cdp.exp_type_list = EXP_TYPE_LIST + # Get info for all models. all_models_info = models_info(models=MODEL_LIST_FULL) @@ -5232,7 +5058,7 @@ self.assert_(hasattr(cdp.mol[0].res[42].spin[0], 'ri_data')) # The dispersion models. - MODELS = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] + MODELS = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] # The grid search size (the number of increments per dimension). GRID_INC = 4 @@ -5497,7 +5323,7 @@ self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False) # The dispersion models. - MODELS = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] + MODELS = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] # The grid search size (the number of increments per dimension). GRID_INC = None @@ -5578,7 +5404,7 @@ # Compare values. if spin_id == ':52@N': if param == 'r1': - if model == MODEL_NOREX_R1RHO: + if model == MODEL_NOREX: self.assertAlmostEqual(value, 1.46328102) elif model == MODEL_DPL94: self.assertAlmostEqual(value, 1.45019848) @@ -5592,7 +5418,7 @@ self.assertAlmostEqual(value, 1.54354372) elif param == 'r2': - if model == MODEL_NOREX_R1RHO: + if model == MODEL_NOREX: self.assertAlmostEqual(value, 11.48040934) elif model == MODEL_DPL94: self.assertAlmostEqual(value, 10.16304887, 6) @@ -5652,7 +5478,7 @@ self.assertAlmostEqual(value, 4909.88110195, 3) elif param == 'chi2': - if model == MODEL_NOREX_R1RHO: + if model == MODEL_NOREX: self.assertAlmostEqual(value, 3363.95829122) elif model == MODEL_DPL94: self.assertAlmostEqual(value, 710.24767560)