Author: bugman
Date: Fri Nov 29 11:45:54 2013
New Revision: 21714
URL: http://svn.gna.org/viewcvs/relax?rev=21714&view=rev
Log:
Created the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system
test.
This is used to demonstrate a failure in the 'R2eff' model when some data is
missing.
Added:
trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py
- copied, changed from r21702,
trunk/test_suite/system_tests/scripts/relax_disp/hansen_data.py
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=21714&r1=21713&r2=21714&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Fri Nov 29 11:45:54 2013
@@ -751,6 +751,69 @@
self.assertAlmostEqual(spin71.dw, 2.00500965887772, 3)
self.assertAlmostEqual(spin71.kex/10000, 2481.10839579804/10000, 3)
self.assertAlmostEqual(spin71.chi2, 15.6595374288635, 3)
+
+
+ def test_hansen_cpmg_data_missing_auto_analysis(self):
+ """Test of the dispersion auto-analysis using Dr. Flemming Hansen's
CPMG data with parts missing.
+
+ This uses the data from Dr. Flemming Hansen's paper at
http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed
relaxation time period.
+ """
+
+ # Set the model.
+ ds.models = [
+ MODEL_R2EFF,
+ MODEL_NOREX,
+ MODEL_CR72
+ ]
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data_missing.py')
+ self.interpreter.state.save('analysis_heights', dir=ds.tmpdir,
force=True)
+
+ # The R20 keys.
+ r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
+ r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
+
+ # The 'No Rex' model checks.
+ self.interpreter.pipe.switch(pipe_name='No Rex')
+ spin70 = return_spin(":70")
+ spin71 = return_spin(":71")
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value
(:71)"))
+ print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)",
spin70.r2[r20_key1], spin71.r2[r20_key1]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)",
spin70.r2[r20_key2], spin71.r2[r20_key2]))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
+ self.assertAlmostEqual(spin70.r2[r20_key1], 10.5340593984683, 3)
+ self.assertAlmostEqual(spin70.r2[r20_key2], 16.1112170102734, 3)
+ self.assertAlmostEqual(spin70.chi2, 8973.84810025761, 3)
+ self.assertAlmostEqual(spin71.r2[r20_key1], 5.83139953954648, 3)
+ self.assertAlmostEqual(spin71.r2[r20_key2], 8.90856319376098, 3)
+ self.assertAlmostEqual(spin71.chi2, 3908.00127830003, 3)
+
+ # The 'CR72' model checks.
+ self.interpreter.pipe.switch(pipe_name='CR72')
+ spin70 = return_spin(":70")
+ spin71 = return_spin(":71")
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value
(:71)"))
+ print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)",
spin70.r2[r20_key1], spin71.r2[r20_key1]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)",
spin70.r2[r20_key2], spin71.r2[r20_key2]))
+ print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA))
+ print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw))
+ print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
+ self.assertAlmostEqual(spin70.r2[r20_key1], 6.97233943292193, 3)
+ self.assertAlmostEqual(spin70.r2[r20_key2], 9.409506394526, 3)
+ self.assertAlmostEqual(spin70.pA, 0.989856804525044, 3)
+ self.assertAlmostEqual(spin70.dw, 5.60889078920945, 3)
+ self.assertAlmostEqual(spin70.kex/10000, 1753.01607073019/10000, 3)
+ self.assertAlmostEqual(spin70.chi2, 53.8382158551706, 3)
+ self.assertAlmostEqual(spin71.r2[r20_key1], 5.003171547206, 3)
+ self.assertAlmostEqual(spin71.r2[r20_key2], 6.90210797727492, 3)
+ self.assertAlmostEqual(spin71.pA, 0.985922406455826, 3)
+ self.assertAlmostEqual(spin71.dw, 2.00500965892672, 3)
+ self.assertAlmostEqual(spin71.kex/10000, 2481.10839579617/10000, 3)
+ self.assertAlmostEqual(spin71.chi2, 15.6595374286822, 3)
def test_hansen_cpmg_data_to_cr72(self):
Copied:
trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py (from
r21702, trunk/test_suite/system_tests/scripts/relax_disp/hansen_data.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py?p2=trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py&p1=trunk/test_suite/system_tests/scripts/relax_disp/hansen_data.py&r1=21702&r2=21714&rev=21714&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/relax_disp/hansen_data.py (original)
+++ trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py
Fri Nov 29 11:45:54 2013
@@ -6,11 +6,12 @@
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
+from specific_analyses.relax_disp.variables import MODEL_NOREX, MODEL_R2EFF
from status import Status; status = Status()
# The dispersion models.
-MODELS = ['LM63']
+MODELS = [MODEL_R2EFF, MODEL_NOREX]
if hasattr(ds, 'models'):
MODELS = ds.models
@@ -38,9 +39,8 @@
# The path to the data files.
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
-# Load the saved base pipe containing R2eff data.
-results.read(data_path+sep+'r2eff_pipe')
-deselect.spin(":4")
+# Load the saved base pipe with the missing data.
+results.read(data_path+sep+'missing_data_pipe')
# Set the nuclear isotope data.
spin.isotope('15N')
r21714 - in /trunk/test_suite/system_tests: relax_disp.py scripts/relax_disp/hansen_data_missing.py