Author: tlinnet
Date: Wed Mar 12 16:14:20 2014
New Revision: 22467
URL: http://svn.gna.org/viewcvs/relax?rev=22467&view=rev
Log:
Added systemtest
Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis().
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is to test the auto_analysis value.write function to write theta and
w_eff values for an R1rho setup.
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=22467&r1=22466&r2=22467&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Wed Mar 12 16:14:20 2014
@@ -3874,3 +3874,84 @@
# Close files
w_eff_file.close()
+
+
+ def test_value_write_calc_rotating_frame_params_auto_analysis(self):
+ """System test of the auto_analysis value.write function to write
theta and w_eff values for an R1rho setup.
+
+ This uses the data of the saved state attached to U{bug
#21344<https://gna.org/bugs/?21344>}.
+ """
+
+ # Load the state.
+ statefile =
status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344.bz2'
+ self.interpreter.state.load(statefile, force=True)
+
+ # Set pipe name, bundle and type.
+ pipe_name = 'base pipe'
+ pipe_bundle = 'relax_disp'
+ pipe_type= 'relax_disp'
+
+ # The path to the data files.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
+
+ # Deselect all spins
+ self.interpreter.deselect.all()
+
+ # Specify spins to be selected.
+ select_spin_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"]
+
+ # Reverse the selection for the spins.
+ for curspin in select_spin_ids:
+ print("Selecting spin %s"%curspin)
+ self.interpreter.deselect.reverse(spin_id=curspin)
+
+ # Read the 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)
+
+ # The dispersion models.
+ MODELS = ['R2eff']
+
+ # 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
+
+ # 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)
+
+ ## Check for file creation
+ # Set filepaths.
+ theta_filepath = ds.tmpdir+sep+MODELS[0]+sep+'theta.out'
+ w_eff_filepath = ds.tmpdir+sep+MODELS[0]+sep+'w_eff.out'
+
+ # Test the files exists.
+ self.assert_(access(theta_filepath, F_OK))
+ self.assert_(access(w_eff_filepath, F_OK))
+
+
r22467 - /trunk/test_suite/system_tests/relax_disp.py