Author: bugman
Date: Tue Oct 7 14:23:31 2014
New Revision: 26181
URL: http://svn.gna.org/viewcvs/relax?rev=26181&view=rev
Log:
Merged revisions 26149-26150 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26149 | tlinnet | 2014-10-05 22:22:35 +0200 (Sun, 05 Oct 2014) | 3 lines
Implemented systemtest Relax_disp.test_dx_map_clustered to cath the missing
creation of a point file.
Bug #22753 (https://gna.org/bugs/index.php?22753): dx.map does not work
when only 1 point is used.
........
r26150 | tlinnet | 2014-10-05 22:22:38 +0200 (Sun, 05 Oct 2014) | 5 lines
Fix for writing out point files, when only one point is used.
The code was testing for > 1 points to be present, before writing out point
files.
Bug #22753 (https://gna.org/bugs/index.php?22753): dx.map does not work
when only 1 point is used.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/pipe_control/opendx.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Oct 7 14:23:31 2014
@@ -1 +1 @@
-/trunk:1-26139,26142-26148
+/trunk:1-26139,26142-26150
Modified: branches/frame_order_cleanup/pipe_control/opendx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/opendx.py?rev=26181&r1=26180&r2=26181&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/opendx.py (original)
+++ branches/frame_order_cleanup/pipe_control/opendx.py Tue Oct 7 14:23:31
2014
@@ -182,7 +182,7 @@
write_general(file_prefix=self.file_prefix, dir=self.dir,
inc=self.inc)
# Create the OpenDX .general and data files for the given point.
- if self.num_points > 1:
+ if self.num_points >= 1:
write_point(file_prefix=self.point_file, dir=self.dir,
inc=self.inc, point=self.point, num_points=self.num_points,
bounds=self.bounds, N=self.n)
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=26181&r1=26180&r2=26181&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 7 14:23:31 2014
@@ -2984,6 +2984,122 @@
# Increment the spin index.
spin_index += 1
+
+
+ def test_dx_map_clustered(self):
+ """Test making dx_map for residues under clustered calculation.
+
+ This uses CPMG data from:
+
+ Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F,
Soendergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE
+ Remeasuring HEWL pK(a) values by NMR spectroscopy: methods,
analysis, accuracy, and implications for theoretical pK(a) calculations.
+ (2011), Proteins: Struct, Funct, Bioinf 79(3):685-702, DOI
10.1002/prot.22886
+ """
+
+ # Define path to data
+ prev_data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'HWebb_KTeilum_Proteins_Struct_Funct_Bioinf_2011'
+
+ # Read data.
+ self.interpreter.results.read(prev_data_path + sep +
'FT_-_CR72_-_min_-_128_-_free_spins')
+
+ # Define temporary folder.
+ result_dir = self.tmpdir
+ #result_dir = None
+
+ # Get residue of interest.
+ cur_spin_id = ":%i@%s"%(52, '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.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', 'pA', 'kex']
+ dx_point_clustered_min = [cur_spin.dw, cur_spin.pA, cur_spin.kex]
+
+ 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 = 'CR72'
+ 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 = []
+ upper = []
+ for i, param_val in enumerate(dx_point_clustered_min):
+ param = dx_params[0]
+ 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))
+
+ # If the number of increments are 2, there will be 3 point
calculations per parameter.
+ # Since we have ordered the lower and upper limits on sides of the
parameter, the middle index should give us the expected global value.
+ dx_param_indexes = dx_inc + 1
+ dx_point_index = dx_inc_sides + 1
+
+ # Find the line number.
+ line = 1
+ for i in range(1, dx_param_indexes + 1):
+ for j in range(1, dx_param_indexes + 1):
+ for k in range(1, dx_param_indexes + 1):
+ if i == dx_point_index and j == dx_point_index and k ==
dx_point_index:
+ line_chi2 = line
+ # Add to line counter.
+ line += 1
+
+ # 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_param_indexes**3
+ print("Nr of chi2 calculations are=%i"%nr_chi2_val)
+ print("Global chi2=%3.3f, Calc_chi=%3.3f, map_line_chi2=%i" %
(pre_chi2, calc_chi2, line_chi2) )
+
+ ## Check for file creation
+ # Set filepaths.
+ 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)
+
+ 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(point_general, F_OK))
+ self.assert_(access(point_point, F_OK))
def test_estimate_r2eff_err(self):
r26181 - in /branches/frame_order_cleanup: ./ pipe_control/opendx.py test_suite/system_tests/relax_disp.py