Author: bugman
Date: Tue Oct 14 13:31:14 2014
New Revision: 26270
URL: http://svn.gna.org/viewcvs/relax?rev=26270&view=rev
Log:
Merged revisions 26244 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26244 | tlinnet | 2014-10-10 17:05:39 +0200 (Fri, 10 Oct 2014) | 10 lines
Created systemtest Relax_disp.test_dx_map_clustered_create_par_file, which
must show that relax is not able to find the local minimum under clustered
conditions.
When creating the map, the map contain chi2 values, which are lower than
the clustered fitted values.
This should not be the case.
I am running a larger map with larger bounds and more increements, which
should show that there exist a minimum in the minimisation space with a lower
chi2 value.
Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate()
does not calculate chi2 value for clustered residues.
Task #7860(https://gna.org/task/index.php?7860): When dx_map is issued,
create a parameter file which maps parameters to chi2 value.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Oct 14 13:31:14 2014
@@ -1 +1 @@
-/trunk:1-26205,26208-26243
+/trunk:1-26205,26208-26244
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=26270&r1=26269&r2=26270&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py Tue
Oct 14 13:31:14 2014
@@ -3044,7 +3044,7 @@
lower = []
upper = []
for i, param_val in enumerate(dx_point_clustered_min):
- param = dx_params[0]
+ param = dx_params[i]
step_val = param_delta * param_val
step_length = step_val * dx_inc_sides
@@ -3115,6 +3115,137 @@
# Assert.
self.assertAlmostEqual(test, pre_chi2, 6)
+
+
+ def test_dx_map_clustered_create_par_file(self):
+ """Test making dx_map for residues under clustered calculation, and
the creation of the parameter file.
+
+ U{Task #7860<https://gna.org/task/index.php?7860>} : When dx_map is
issued, create a parameter file which maps parameters to chi2 value.
+
+ This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride).
+ """
+
+ # Define path to data
+ prev_data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+'surface_chi2_clustered_fitting'
+
+ # Read data.
+ self.interpreter.results.read(prev_data_path + sep +
'coMDD_-_TSMFK01_-_min_-_32_-_free_spins.bz2')
+
+ # Get residue of interest.
+ cur_spin_id = ":%i@%s"%(65, 'N')
+ cur_spin_id_str = cur_spin_id .replace('#', '_').replace(':',
'_').replace('@', '_')
+
+ # Get the spin container.
+ cur_spin = return_spin(cur_spin_id)
+
+ # Get the chi2 value
+ pre_chi2 = cur_spin.chi2
+
+ # Then do a local minimisation.
+ #self.interpreter.select.spin(":%i@%s"%(2, 'N'))
+ self.interpreter.minimise.calculate()
+
+ # Get the chi2 value after calculation.
+ calc_chi2 = cur_spin.chi2
+
+ # Assert calculation is equal.
+ self.assertAlmostEqual(pre_chi2, calc_chi2)
+
+ # Define dx.map settings.
+ dx_inc = 2
+ dx_inc_sides = dx_inc / 2
+
+ dx_params = ['dw', 'k_AB', 'r2a']
+ dx_point_clustered_min = [cur_spin.dw, cur_spin.k_AB,
cur_spin.r2a['SQ CPMG - 499.86214000 MHz']]
+
+ print("Params for dx map is")
+ print(dx_params)
+ print("Point param for dx map is, with chi2=%3.3f"%pre_chi2)
+ print(dx_point_clustered_min)
+
+ # Define file_names.
+ cur_model = 'TSMFK01'
+ file_name_map = "%s_map%s" % (cur_model, cur_spin_id_str)
+ file_name_point = "%s_point%s" % (cur_model, cur_spin_id_str)
+
+ # Step-size of parameter is 10 %
+ param_delta = 0.1
+
+ # Determine bounds for lower and upper
+ #lower = [0.0, 0.0, 5.0]
+ #upper = [20.0, 6.0, 15.0]
+
+ lower = []
+ upper = []
+ for i, param_val in enumerate(dx_point_clustered_min):
+ param = dx_params[i]
+ step_val = param_delta * param_val
+ step_length = step_val * dx_inc_sides
+
+ # Calculate value
+ low_val = param_val - step_length
+ lower.append(low_val)
+
+ upp_val = param_val + step_length
+ upper.append(upp_val)
+
+ print("For param %s, lower=%3.3f, upper=%3.3f, step_value=%3.3f,
steps=%i, centered at=%3.3f"% (param, low_val, upp_val, step_val, dx_inc,
param_val))
+
+ # Define temporary folder.
+ result_dir = self.tmpdir
+
+ # For testing.
+ #result_dir = None
+ #lower = None
+ #upper = None
+ #self.interpreter.relax_disp.cluster(cluster_id='free spins',
spin_id=cur_spin_id)
+
+ # Then do the map.
+ self.interpreter.dx.map(params=dx_params, map_type='Iso3D',
spin_id=cur_spin_id, inc=dx_inc, lower=lower, upper=upper, axis_incs=10,
file_prefix=file_name_map, dir=result_dir, point=dx_point_clustered_min,
point_file=file_name_point)
+
+ # Print where to locate values.
+ nr_chi2_val = (dx_inc + 1)**3
+ print("Nr of chi2 calculations are=%i"%nr_chi2_val)
+ print("Global chi2=%3.3f, Calc_chi=%3.3f" % (pre_chi2, calc_chi2) )
+
+ ## Check for file creation
+ # Set filepaths.
+ map_name = get_file_path(file_name=file_name_map, dir=result_dir)
+ map_cfg = get_file_path(file_name=file_name_map+".cfg",
dir=result_dir)
+ map_net = get_file_path(file_name=file_name_map+".net",
dir=result_dir)
+ map_general = get_file_path(file_name=file_name_map+".general",
dir=result_dir)
+ map_par = get_file_path(file_name=file_name_map+".par",
dir=result_dir)
+
+ point_general = get_file_path(file_name=file_name_point+".general",
dir=result_dir)
+ point_point = get_file_path(file_name=file_name_point,
dir=result_dir)
+
+ # Test the files exists.
+ self.assert_(access(map_cfg, F_OK))
+ self.assert_(access(map_net, F_OK))
+ self.assert_(access(map_general, F_OK))
+ self.assert_(access(map_par, F_OK))
+ self.assert_(access(point_general, F_OK))
+ self.assert_(access(point_point, F_OK))
+
+ print("\nParams for dx map is")
+ print(dx_params)
+ print("Point param for dx map is, with chi2=%3.3f"%pre_chi2)
+ print(dx_point_clustered_min, "\n")
+
+ # Open the parameter chi2 file, and assert the chi2 value in the
sorted parameter file is not lower that than the global minimisation.
+ get_data = extract_data(file=map_par)
+
+ # Extract line 1, column 9.
+ test = float(get_data[1][9])
+
+ # Print data if map contain a lower value than the global minimised
value.
+ if test < pre_chi2:
+ print("\nInitial clustered minimised chi2 value is=%3.3f,
whereby the minimum map value is=%3.3f\n" % (pre_chi2, test))
+ for line in get_data:
+ print(line)
+
+ # Assert that the initial global chi2 is lower than the map value.
+ self.assert_(pre_chi2 < test)
def test_estimate_r2eff_err(self):
r26270 - in /branches/frame_order_cleanup: ./ test_suite/system_tests/relax_disp.py