r24073 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py -- June 18, 2014 - 10:35

Author: tlinnet
Date: Wed Jun 18 10:35:42 2014
New Revision: 24073

URL: http://svn.gna.org/viewcvs/relax?rev=24073&view=rev
Log:
Implemented systemtest test_r1rho_kjaergaard_missing_r1, for safety check if 
R1 data is not loaded.

The systemtest passes, so target function is safe.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
models for Clustered analysis.

Modified:
    branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24073&r1=24072&r2=24073&view=diff
==============================================================================
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py      
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py      Wed 
Jun 18 10:35:42 2014
@@ -60,6 +60,7 @@
                 "test_m61_exp_data_to_m61",
                 "test_r1rho_kjaergaard_auto",
                 "test_r1rho_kjaergaard_man",
+                "test_r1rho_kjaergaard_missing_r1",
                 "test_value_write_calc_rotating_frame_params_auto_analysis"
             ]
 
@@ -4587,6 +4588,80 @@
         
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'theta.out',
 F_OK))
 
 
+    def test_r1rho_kjaergaard_missing_r1(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>}.
+
+        This uses the automatic analysis, with missing loading R1.
+
+        """
+
+        # Cluster residues
+        cluster_ids = [
+        ":13@N",
+        ":15@N",
+        ":16@N",
+        ":25@N",
+        ":26@N",
+        ":28@N",
+        ":39@N",
+        ":40@N",
+        ":41@N",
+        ":43@N",
+        ":44@N",
+        ":45@N",
+        ":49@N",
+        ":52@N",
+        ":53@N"]
+
+        # Load the data.
+        self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False)
+
+        # The dispersion models.
+        MODELS = ['R2eff', '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'
+
+        # Execute the auto-analysis (fast).
+        # Standard parameters are: func_tol=1e-25, grad_tol=None, 
max_iter=10000000,
+        OPT_FUNC_TOL = 1e-1
+        relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
+        OPT_MAX_ITERATIONS = 1000
+        relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS
+
+        result_dir_name = ds.tmpdir
+
+        # Make all spins free
+        for curspin in cluster_ids:
+            self.interpreter.relax_disp.cluster('free spins', curspin)
+            # Shut them down
+            self.interpreter.deselect.spin(spin_id=curspin, change_all=False)
+
+        # Select only a subset of spins for global fitting
+        #self.interpreter.select.spin(spin_id=':41@N', change_all=False)
+        #self.interpreter.relax_disp.cluster('model_cluster', ':41@N')
+
+        #self.interpreter.select.spin(spin_id=':40@N', change_all=False)
+        #self.interpreter.relax_disp.cluster('model_cluster', ':40@N')
+
+        self.interpreter.select.spin(spin_id=':52@N', change_all=False)
+        #self.interpreter.relax_disp.cluster('model_cluster', ':52@N')
+
+        # Run the analysis.
+        relax_disp.Relax_disp(pipe_name=ds.pipe_name, 
pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, 
grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL)
+
+        # Check the kex value of residue 52
+        #self.assertAlmostEqual(cdp.mol[0].res[41].spin[0].kex, 
ds.ref[':52@N'][6])
+
+
     def test_r2eff_read(self):
         """Test the operation of the relax_disp.r2eff_read user function."""