Author: tlinnet
Date: Fri Apr 25 15:38:04 2014
New Revision: 22855
URL: http://svn.gna.org/viewcvs/relax?rev=22855&view=rev
Log:
Added systemtest for setting R20 from minimum R2eff before grid search.
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.
Systemtest: -s Relax_disp.test_sod1wt_t25_set_grid_r20_from_min_r2eff.
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=22855&r1=22854&r2=22855&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Fri Apr 25 15:38:04 2014
@@ -31,7 +31,7 @@
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
from pipe_control.mol_res_spin import return_spin, spin_loop
-from specific_analyses.relax_disp.data import generate_r20_key,
get_curve_type
+from specific_analyses.relax_disp.data import generate_r20_key,
get_curve_type, loop_exp_frq_offset_point, return_param_key_from_data,
set_grid_r20_from_min_r2eff
from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_IT99,
MODEL_LM63, MODEL_M61B, MODEL_NOREX, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_R2EFF
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -3554,6 +3554,85 @@
#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(0,2)
+ 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.
+ set_grid_r20_from_min_r2eff(force=False, verbosity=1)
+
+ # 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("")
+
+
def test_sprangers_data_to_mmq_cr72(self, model=None):
"""Test the 'MMQ CR72' model fitting against Remco Sprangers' ClpP
data.
r22855 - /trunk/test_suite/system_tests/relax_disp.py