Author: tlinnet
Date: Mon Apr 28 16:09:25 2014
New Revision: 22867
URL: http://svn.gna.org/viewcvs/relax?rev=22867&view=rev
Log:
Renamed system test to reflect what it is testing.
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.
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=22867&r1=22866&r2=22867&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Apr 28 16:09:25 2014
@@ -3384,6 +3384,149 @@
self.assertEqual(cdp.mol[0].res[2].spin[0].ri_data['R2eff.600'],
7.2385)
+ def test_set_grid_r20_from_min_r2eff_cpmg(self):
+ """Test speeding up grid search. Support requst sr #3151
U{https://gna.org/support/index.php?3151}.
+
+ User function to set the R20 parameters in the default grid search
using the minimum R2eff value.
+
+ Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
+ 'SOD1-WT' CPMG data to the CR72 dispersion model.
+
+ This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}. This is CPMG data with a fixed
relaxation time period recorded at fields of 500 and 600MHz.
+ Data is for experiment at 25 degree Celcius.
+ """
+
+ # Base data setup.
+ pipe_name = 'base pipe'
+ pipe_type = 'relax_disp'
+ pipe_name_r2eff = "%s_R2eff"%(pipe_name)
+ 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
+ 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
+ MODEL = "CR72"
+
+ # 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
+ self.interpreter.relax_disp.select_model(model=MODEL)
+
+ # Set the R20 parameters in the default grid search using the
minimum R2eff value.
+ self.interpreter.relax_disp.set_grid_r20_from_min_r2eff(force=False)
+
+ # 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
+ spin_params = spin.params
+ # 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
+ self.assert_(spin.r2[r20_key_600] > 0.0)
+ self.assert_(spin.r2[r20_key_500] > 0.0)
+
+ # Loop over the experiment settings.
+ r2eff_600 = []
+ r2eff_500 = []
+ for exp_type, frq, offset, point, ei, mi, oi, di in
loop_exp_frq_offset_point(return_indices=True):
+ # 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
+ 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
+ r2eff_600.sort()
+ r2eff_500.sort()
+
+ # 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))
+ print("")
+
+ print("For r20 500MHz min r2eff=%3.3f."%(min(r2eff_500)))
+ print(r2eff_500)
+ self.assertEqual(spin.r2[r20_key_500], min(r2eff_500))
+ print("")
+
+ print("###########################################")
+ print("Trying GRID SEARCH for minimum R2eff values")
+
+ ### 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
+ 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
+ self.interpreter.relax_disp.select_model(model=MODEL)
+
+ # 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("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
+ self.assertEqual(spin.r2[r20_key_600], 10.00)
+ self.assertEqual(spin.r2[r20_key_500], 10.00)
+ self.assertEqual(spin.pA, 0.5)
+ self.assertEqual(spin.dw, 0.0)
+ self.assertEqual(spin.kex, 10000.0)
+
+ print("###########################################")
+ print("Trying GRID SEARCH for standard R2eff values")
+
+ ### 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
+ # The grid search size (the number of increments per dimension).
+ GRID_INC = 5
+
+ # 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_r2eff,
results_dir=ds.tmpdir, models=[MODEL], grid_inc=GRID_INC, mc_sim_num=MC_NUM,
modsel=MODSEL, set_grid_r20=True)
+
+
def test_sod1wt_t25_bug_21954_order_error_analysis(self):
"""Error analysis of SOD1-WT CPMG. From paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}.
@@ -3552,110 +3695,6 @@
# Save disp graph to temp
#self.interpreter.relax_disp.plot_disp_curves(dir="~"+sep+"test",
num_points=1000, extend=500.0, force=True)
-
-
- def test_sod1wt_t25_set_grid_r20_from_min_r2eff(self):
- """Test speeding up grid search. Support requst sr #3151
U{https://gna.org/support/index.php?3151}.
-
- User function to set the R20 parameters in the default grid search
using the minimum R2eff value.
-
- Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
- 'SOD1-WT' CPMG data to the CR72 dispersion model.
-
- This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}. This is CPMG data with a fixed
relaxation time period recorded at fields of 500 and 600MHz.
- Data is for experiment at 25 degree Celcius.
- """
-
- # Base data setup.
- pipe_name = 'base pipe'
- pipe_type = 'relax_disp'
- pipe_name_r2eff = "%s_R2eff"%(pipe_name)
- 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
- 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
- MODEL = "CR72"
-
- # 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
- self.interpreter.relax_disp.select_model(model=MODEL)
-
- # Set the R20 parameters in the default grid search using the
minimum R2eff value.
- self.interpreter.relax_disp.set_grid_r20_from_min_r2eff(force=False)
-
- # 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("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
- self.assert_(spin.r2[r20_key_600] > 0.0)
- self.assert_(spin.r2[r20_key_500] > 0.0)
-
- # Loop over the experiment settings.
- r2eff_600 = []
- r2eff_500 = []
- for exp_type, frq, offset, point, ei, mi, oi, di in
loop_exp_frq_offset_point(return_indices=True):
- # 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
- 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
- r2eff_600.sort()
- r2eff_500.sort()
-
- # 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))
- print("")
-
- print("For r20 500MHz min r2eff=%3.3f."%(min(r2eff_500)))
- print(r2eff_500)
- self.assertEqual(spin.r2[r20_key_500], min(r2eff_500))
- print("")
-
- # 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
- # The grid search size (the number of increments per dimension).
- GRID_INC = 5
-
- # 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_r2eff,
results_dir=ds.tmpdir, models=[MODEL], grid_inc=GRID_INC, mc_sim_num=MC_NUM,
modsel=MODSEL, set_grid_r20=True)
def test_sprangers_data_to_mmq_cr72(self, model=None):
r22867 - /trunk/test_suite/system_tests/relax_disp.py