Author: tlinnet
Date: Tue Apr 29 15:38:33 2014
New Revision: 22878
URL: http://svn.gna.org/viewcvs/relax?rev=22878&view=rev
Log:
Fix for systemtest Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg.
Feature request: #3151, (https://gna.org/support/index.php?3151) - User
function to set the R20 parameters in the default grid search using the
minimum R2eff value.
Fixed values for testing was added.
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=22878&r1=22877&r2=22878&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Apr 29 15:38:33 2014
@@ -3403,19 +3403,19 @@
select_spin_index = range(0,1)
self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type,
pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index)
- # Generate r20 keu
+ # Generate r20 key.
r20_key_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=599.8908617*1E6)
r20_key_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=499.862139*1E6)
- ## Now prepare for MODEL calculation
+ ## Now prepare for MODEL calculation.
MODEL = "CR72"
- # Change pipe
+ # Change pipe.
pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL)
self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
- # Then select model
+ # Then select model.
self.interpreter.relax_disp.select_model(model=MODEL)
# Set the R20 parameters in the default grid search using the
minimum R2eff value.
@@ -3423,15 +3423,21 @@
# Test result, for normal run.
for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True,
return_id=True, skip_desel=True):
- # Get the spin_params
+ # Get the spin_params.
spin_params = spin.params
- # Print out
+
+ # Defined fixed values for testing.
+ if spin_id == ":10@N":
+ self.assertEqual(spin.r2[r20_key_600], 20.282732526087106)
+ self.assertEqual(spin.r2[r20_key_500], 18.475299724356649)
+
+ # Print out.
print("r2_600=%2.2f r2_500=%2.2f spin_id=%s resi=%i
resn=%s"%(spin.r2[r20_key_600], spin.r2[r20_key_500], spin_id, resi, resn))
# Testing the r2 values for the different fields are not the
same.
self.assert_(spin.r2[r20_key_600] != spin.r2[r20_key_500])
- # Test values are larger than 0
+ # Test values are larger than 0.
self.assert_(spin.r2[r20_key_600] > 0.0)
self.assert_(spin.r2[r20_key_500] > 0.0)
@@ -3442,18 +3448,18 @@
# Create the data key.
data_key = return_param_key_from_data(exp_type=exp_type,
frq=frq, offset=offset, point=point)
- # Extract the r2 eff data
+ # Extract the r2 eff data.
r2eff = spin.r2eff[data_key]
if frq == 599.8908617*1E6:
r2eff_600.append(r2eff)
elif frq == 499.862139*1E6:
r2eff_500.append(r2eff)
- # Sort values
+ # Sort values.
r2eff_600.sort()
r2eff_500.sort()
- # Test values again
+ # Test values again.
print("For r20 600MHz min r2eff=%3.3f."%(min(r2eff_600)))
print(r2eff_600)
self.assertEqual(spin.r2[r20_key_600], min(r2eff_600))
@@ -3467,31 +3473,31 @@
print("###########################################")
print("Trying GRID SEARCH for minimum R2eff values")
- ### Test just the Grid search
+ ### Test just the Grid search.
GRID_INC = 5
self.interpreter.grid_search(lower=None, upper=None, inc=GRID_INC,
constraints=True, verbosity=1)
- ### Then test the value.set function
- # Change pipe
+ ### Then test the value.set function.
+ # Change pipe.
pipe_name_MODEL = "%s_%s_2"%(pipe_name, MODEL)
self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
- # Then select model
+ # Then select model.
self.interpreter.relax_disp.select_model(model=MODEL)
- # Then set the standard parameter values
+ # Then set the standard parameter values.
for param in spin_params:
print("Setting standard parameter for param: %s"%param)
self.interpreter.value.set(param=param, index=None)
# Test result, for normal run.
for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True,
return_id=True, skip_desel=True):
- # Print out
+ # Print out.
print("r2_600=%2.2f r2_500=%2.2f pA=%2.2f, dw=%2.2f, kex=%2.2f,
spin_id=%s resi=%i resn=%s"%(spin.r2[r20_key_600], spin.r2[r20_key_500],
spin.pA, spin.dw, spin.kex, spin_id, resi, resn))
- # Testing the r2 values
+ # Testing the r2 values.
self.assertEqual(spin.r2[r20_key_600], 10.00)
self.assertEqual(spin.r2[r20_key_500], 10.00)
self.assertEqual(spin.pA, 0.5)
@@ -3501,12 +3507,12 @@
print("###########################################")
print("Trying GRID SEARCH for standard R2eff values")
- ### Test just the Grid search
+ ### Test just the Grid search.
GRID_INC = 5
self.interpreter.grid_search(lower=None, upper=None, inc=GRID_INC,
constraints=True, verbosity=1)
- ### Run auto_analysis
+ ### Run auto_analysis.
# The grid search size (the number of increments per dimension).
GRID_INC = 5
@@ -3517,7 +3523,7 @@
MODSEL = 'AIC'
# Execute the auto-analysis (fast).
- # Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
+ # 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
r22878 - /trunk/test_suite/system_tests/relax_disp.py