Author: bugman
Date: Fri Oct 18 12:27:28 2013
New Revision: 21171
URL: http://svn.gna.org/viewcvs/relax?rev=21171&view=rev
Log:
Created the new Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric system
test.
This will be used to test a new feature whereby pure numeric models will be
used in the
auto-analysis.
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=21171&r1=21170&r2=21171&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Fri Oct 18
12:27:28 2013
@@ -31,7 +31,7 @@
import dep_check
from pipe_control.mol_res_spin import spin_loop
from specific_analyses.relax_disp.disp_data import get_curve_type
-from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_FULL, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LM63, MODEL_M61B,
MODEL_NOREX, MODEL_R2EFF
+from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_FULL, MODEL_IT99, MODEL_LIST_CPMG, 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
@@ -410,6 +410,84 @@
MODEL_CR72,
MODEL_IT99
]
+
+ # 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.py')
+
+ # The 'No Rex' model checks.
+ self.interpreter.pipe.switch(pipe_name='No Rex')
+ spin70 = cdp.mol[0].res[0].spin[0]
+ spin71 = cdp.mol[0].res[1].spin[0]
+ 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[0],
spin71.r2[0]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[1],
spin71.r2[1]))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
+ self.assertAlmostEqual(spin70.r2[0], 10.5340573632181, 4)
+ self.assertAlmostEqual(spin70.r2[1], 16.1113049920324, 4)
+ self.assertAlmostEqual(spin70.chi2, 2832.28562307, 4)
+ self.assertAlmostEqual(spin71.r2[0], 5.83137814994754, 4)
+ self.assertAlmostEqual(spin71.chi2, 73.6219146835821, 4)
+
+ # The 'LM63' model checks.
+ self.interpreter.pipe.switch(pipe_name='LM63')
+ spin70 = cdp.mol[0].res[0].spin[0]
+ spin71 = cdp.mol[0].res[1].spin[0]
+ 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[0],
spin71.r2[0]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[1],
spin71.r2[1]))
+ print("%-20s %20.15g %20.15g" % ("phi_ex", spin70.phi_ex,
spin71.phi_ex))
+ 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[0], 6.7725779040626, 4)
+ self.assertAlmostEqual(spin70.r2[1], 6.6495102881274, 4)
+ self.assertAlmostEqual(spin70.phi_ex, 0.308228782539112, 4)
+ self.assertAlmostEqual(spin70.kex/10000, 4644.35027966526/10000, 4)
+ self.assertAlmostEqual(spin70.chi2, 137.64638621224, 4)
+ self.assertAlmostEqual(spin71.r2[0], 4.92986568906445, 4)
+ self.assertAlmostEqual(spin71.phi_ex, 0.0595701347673553, 4)
+ self.assertAlmostEqual(spin71.kex/10000, 2566.66176813506/10000, 4)
+ self.assertAlmostEqual(spin71.chi2, 2.31424715490254, 4)
+
+ # The 'CR72' model checks. These models have not reached the minima
due to the low quality optimisation!
+ self.interpreter.pipe.switch(pipe_name='CR72')
+ spin70 = cdp.mol[0].res[0].spin[0]
+ spin71 = cdp.mol[0].res[1].spin[0]
+ 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[0],
spin71.r2[0]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[1],
spin71.r2[1]))
+ 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[0], 6.97532271825192, 4)
+ self.assertAlmostEqual(spin70.r2[1], 9.45051817816538, 4)
+ self.assertAlmostEqual(spin70.pA, 0.989800346795472, 4)
+ self.assertAlmostEqual(spin70.dw, 5.61326926915313, 4)
+ self.assertAlmostEqual(spin70.kex/10000, 1713.02295468519/10000, 4)
+ self.assertAlmostEqual(spin70.chi2, 17.3955972313639, 4)
+ self.assertAlmostEqual(spin71.r2[0], 0.589453313816438, 2)
+ self.assertAlmostEqual(spin71.pA, 0.500005674625128, 2)
+ self.assertAlmostEqual(spin71.dw, 199.873875627265, 2)
+ self.assertAlmostEqual(spin71.kex, 10.7154862578618, 2)
+ self.assertAlmostEqual(spin71.chi2, 57.9468501661789, 2)
+
+
+ def test_hansen_cpmg_data_auto_analysis_numeric(self):
+ """Test of the numeric model only dispersion auto-analysis using Dr.
Flemming Hansen's CPMG data.
+
+ 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 and numeric flag.
+ ds.models = [
+ MODEL_NOREX,
+ MODEL_CR72,
+ MODEL_NS_CPMG_2SITE_EXPANDED
+ ]
+ ds.numeric_flag = True
# 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.py')
Modified:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py?rev=21171&r1=21170&r2=21171&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
Fri Oct 18 12:27:28 2013
@@ -17,6 +17,12 @@
# The temporary directory, if needed.
if not hasattr(ds, 'tmpdir'):
ds.tmpdir = 'temp'
+
+# The numeric flag.
+if hasattr(ds, 'numeric_flag') and ds.numeric_flag:
+ model_class = 'numeric'
+else:
+ model_class = 'mixed'
# The grid search size (the number of increments per dimension).
GRID_INC = 5
@@ -54,7 +60,7 @@
Relax_disp.opt_max_iterations = 10000
# Do not change!
-Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM)
+Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM,
model_class=model_class)
# Save the program state.
state.save('devnull', force=True)
r21171 - in /branches/relax_disp/test_suite/system_tests: relax_disp.py scripts/relax_disp/hansen_data.py