Author: tlinnet
Date: Wed Jul 30 22:27:23 2014
New Revision: 24861
URL: http://svn.gna.org/viewcvs/relax?rev=24861&view=rev
Log:
Added systemtest Relax_disp.test_r1rho_kjaergaard_auto_check_graphs, to check
that the contents of all combinations of graphs are consistent.
The systemtest actual show that the error is changing per run-through.
This is a bug, which should be corrected.
sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
Modified:
branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
Modified: branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/test_suite/system_tests/relax_disp.py?rev=24861&r1=24860&r2=24861&view=diff
==============================================================================
--- branches/r1rho_plotting/test_suite/system_tests/relax_disp.py
(original)
+++ branches/r1rho_plotting/test_suite/system_tests/relax_disp.py Wed
Jul 30 22:27:23 2014
@@ -4745,6 +4745,55 @@
# Check the kex value of residue 52
#self.assertAlmostEqual(cdp.mol[0].res[41].spin[0].kex,
ds.ref[':52@N'][6])
+
+ def test_r1rho_kjaergaard_auto_check_graphs(self):
+ """Check of plot_disp_curves() function, after optimisation of the
Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments
using the 'R2eff' 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.
+
+ """
+
+ # Cluster residues
+ cluster_ids = [
+ ":52@N"]
+
+ # Load the data.
+ self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids)
+
+ # The dispersion models.
+ MODELS = [MODEL_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
+
+ 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)
+
+ self.interpreter.select.spin(spin_id=':52@N', change_all=False)
+
+ # 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 graphs produced.
graph_comb = [
[Y_AXIS_R2_EFF, X_AXIS_DISP, INTERPOLATE_DISP],
@@ -4754,7 +4803,7 @@
]
# Define expected folder names.
- result_folders = MODELS + ['final']
+ result_folders = MODELS
# Assign spin_id.
spin_id = ':52@N'
@@ -4783,33 +4832,54 @@
result_dir_name = ds.tmpdir
# Loop through all possible combinations of y_axis, x_axis and
interpolation.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'+sep+'check_graphs'
i = 1
- for y_axis in y_axis_types:
- for x_axis in x_axis_types:
- for interpolate in interpolate_types:
- # Determine file name:
- file_name_ini =
return_grace_file_name_ini(y_axis=y_axis, x_axis=x_axis,
interpolate=interpolate)
-
- # Make the file name.
- file_name = "%s%s.agr" % (file_name_ini,
spin_id.replace('#', '_').replace(':', '_').replace('@', '_'))
-
- # Set result folder.
- result_folder = "%i"%(i)
-
- # Write the curves.
- dir = result_dir_name+sep+result_folder
- print("Plotting combination of %s, %s, %s"%(y_axis,
x_axis, interpolate))
- self.interpreter.relax_disp.plot_disp_curves(dir=dir,
y_axis=y_axis, x_axis=x_axis, interpolate=interpolate, force=False)
-
- # Get the file path.
- file_path = get_file_path(file_name, dir)
-
- # Test the plot file exists.
- print("Testing file access to graph: %s"%file_path)
- self.assert_(access(file_path, F_OK))
-
- # Add to counter.
- i += 1
+
+ for result_folder in result_folders:
+ for y_axis in y_axis_types:
+ for x_axis in x_axis_types:
+ for interpolate in interpolate_types:
+ # Determine file name:
+ file_name_ini =
return_grace_file_name_ini(y_axis=y_axis, x_axis=x_axis,
interpolate=interpolate)
+
+ # Make the file name.
+ file_name = "%s%s.agr" % (file_name_ini,
spin_id.replace('#', '_').replace(':', '_').replace('@', '_'))
+
+ # Set result folder.
+ dir_folder = "%i"%(i)
+
+ # Write the curves.
+ dir = result_dir_name+sep+result_folder+dir_folder
+ print("Plotting combination of %s, %s, %s"%(y_axis,
x_axis, interpolate))
+
self.interpreter.relax_disp.plot_disp_curves(dir=dir, y_axis=y_axis,
x_axis=x_axis, interpolate=interpolate, force=True)
+
+ # Get the file path.
+ file_path = get_file_path(file_name, dir)
+
+ # Test the plot file exists.
+ print("Testing file access to graph: %s"%file_path)
+ self.assert_(access(file_path, F_OK))
+
+ # Now open, and compare content, line by line.
+ file_prod = open(file_path)
+ lines_prod = file_prod.readlines()
+ file_prod.close()
+
+ # Define file to compare against.
+ dir_comp = data_path+sep+result_folder+sep+dir_folder
+ file_path_comp = get_file_path(file_name, dir_comp)
+ file_comp = open(file_path_comp)
+ lines_comp = file_comp.readlines()
+ file_comp.close()
+
+ # Assert number of lines is equal.
+ self.assertEqual(len(lines_prod), len(lines_comp))
+ for i in range(len(lines_prod)):
+ # Make the string test
+ self.assertEqual(lines_prod[i], lines_comp[i])
+
+ # Add to counter.
+ i += 1
def test_r1rho_kjaergaard_man(self):
r24861 - /branches/r1rho_plotting/test_suite/system_tests/relax_disp.py