Author: bugman
Date: Tue Oct 15 18:18:30 2013
New Revision: 21121
URL: http://svn.gna.org/viewcvs/relax?rev=21121&view=rev
Log:
Converted the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test
to not use the auto-analysis.
The test has been renamed to
Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site. The optimisation
is now for the cluster and has been severely cut back. The 'MQ NS CPMG
2-site' model appears to be
rubbish anyway - it looks to be indeterminate with multiple solutions, and
possibly infinite lines
of solutions. The test now passes, and quickly.
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.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=21121&r1=21120&r2=21121&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Tue Oct 15
18:18:30 2013
@@ -1491,48 +1491,64 @@
self.assertEqual(cdp.mol[0].res[2].spin[0].ri_data['R2eff.600'],
7.2385)
- def test_sprangers_cpmg_data_auto_analysis(self):
- """Test of the dispersion auto-analysis using Remco Sprangers' MQ
CPMG data.
+ def test_sprangers_data_to_mq_ns_cpmg_2site(self, model=None):
+ """Test the 'MQ NS CPMG 2-site' model fitting against Remco
Sprangers' ClpP data.
This uses the data from Remco Sprangers' paper at
http://dx.doi.org/10.1073/pnas.0507370102. This is MQ CPMG data with a fixed
relaxation time period.
"""
- # The models to optimise.
- ds.models = ['R2eff', 'No Rex', 'MQ NS CPMG 2-site']
-
- # Execute the script.
- self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'sprangers_data.py')
-
- # The 'No Rex' model checks.
- self.interpreter.pipe.switch(pipe_name='No Rex')
+ # Reset.
+ self.interpreter.reset()
+
+ # Create the data pipe and load the base data.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Sprangers_ClpP'
+ self.interpreter.state.load(data_path+sep+'r2eff_values')
+
+ # The model data pipe.
+ model = 'MQ NS CPMG 2-site'
+ self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to=model,
bundle_to='relax_disp')
+ self.interpreter.pipe.switch(pipe_name=model)
+
+ # Set the model.
+ self.interpreter.relax_disp.select_model(model=model)
+
+ # Cluster everything.
+ self.interpreter.relax_disp.cluster(cluster_id='all',
spin_id=":135-137")
+
+ # Copy the data.
+ self.interpreter.value.copy(pipe_from='R2eff', pipe_to=model,
param='r2eff')
+
+ # Alias the spins.
spin135S = cdp.mol[0].res[0].spin[0]
spin135F = cdp.mol[0].res[0].spin[1]
spin137S = cdp.mol[0].res[1].spin[0]
spin137F = cdp.mol[0].res[1].spin[1]
- print("\n\nOptimised parameters:\n")
- print("%-20s %-20s %-20s %-20s %-20s" % ("Parameter", "Value
(:135@S)", "Value (:135@F)", "Value (:137@S)", "Value (:137@F)"))
- print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("R2 (500 MHz)",
spin135S.r2[0], spin135F.r2[0], spin137S.r2[0], spin137F.r2[0]))
- print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("R2 (800 MHz)",
spin135S.r2[1], spin135F.r2[1], spin137S.r2[1], spin137F.r2[1]))
- print("%-20s %20.15g %20.15g %20.15g %20.15g\n" % ("chi2",
spin135S.chi2, spin135F.chi2, spin137S.chi2, spin137F.chi2))
- self.assertAlmostEqual(spin135S.r2[0], 33.9759609066454, 4)
- self.assertAlmostEqual(spin135S.r2[1], 43.0969094834547, 4)
- self.assertAlmostEqual(spin135S.chi2, 3969.76481864137, 4)
- self.assertAlmostEqual(spin135F.r2[0], 47.552576922923, 4)
- self.assertAlmostEqual(spin135F.r2[1], 65.0985264581959, 4)
- self.assertAlmostEqual(spin135F.chi2, 3815.60336919813, 4)
- self.assertAlmostEqual(spin137S.r2[0], 32.2534843780118, 4)
- self.assertAlmostEqual(spin137S.r2[1], 42.3438098884568, 4)
- self.assertAlmostEqual(spin137S.chi2, 5059.72438767579, 4)
- self.assertAlmostEqual(spin137F.r2[0], 51.8197781054955, 4)
- self.assertAlmostEqual(spin137F.r2[1], 66.2604887530423, 4)
- self.assertAlmostEqual(spin137F.chi2, 1764.08570485219, 4)
-
- # The 'MQ NS 2-site' model checks.
- self.interpreter.pipe.switch(pipe_name='MQ NS 2-site')
- spin135S = cdp.mol[0].res[0].spin[0]
- spin135F = cdp.mol[0].res[0].spin[1]
- spin137S = cdp.mol[0].res[1].spin[0]
- spin137F = cdp.mol[0].res[1].spin[1]
+
+ # Set the cluster specific parameters (only for the first spin).
+ spin135S.pA = 0.500311298403094
+ spin135S.kex = 59.5551680542025
+
+ # Set the initial parameter values.
+ spin135S.r2 = [ 2.89494989792968, 12.6694205621436]
+ spin135S.dw = 1.47777783753308
+ spin135S.dwH = 1.0880818550171
+
+ spin135F.r2 = [ 41.907752972063, 58.1518607839796]
+ spin135F.dw = 0.419799242782033
+ spin135F.dwH = 1.27742823131436
+
+ spin137S.r2 = [ 0.0736711146623223, 13.8168225329927]
+ spin137S.dw = 2.4030348485243
+ spin137S.dwH = 0.00271978588774347
+
+ spin137F.r2 = [ 45.2885284912096, 57.8347181561312]
+ spin137F.dw = 1.5929498838754
+ spin137F.dwH = 0.00605967407110987
+
+ # Low precision optimisation.
+ self.interpreter.minimise(min_algor='simplex', line_search=None,
hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None,
max_iter=100, constraints=True, scaling=True, verbosity=1)
+
+ # Printout.
print("\n\nOptimised parameters:\n")
print("%-20s %-20s %-20s %-20s %-20s" % ("Parameter", "Value
(:135@S)", "Value (:135@F)", "Value (:137@S)", "Value (:137@F)"))
print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("R2 (500 MHz)",
spin135S.r2[0], spin135F.r2[0], spin137S.r2[0], spin137F.r2[0]))
@@ -1542,34 +1558,42 @@
print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("dwH",
spin135S.dwH, spin135F.dwH, spin137S.dwH, spin137F.dwH))
print("%-20s %20.15g %20.15g %20.15g %20.15g" % ("kex",
spin135S.kex, spin135F.kex, spin137S.kex, spin137F.kex))
print("%-20s %20.15g %20.15g %20.15g %20.15g\n" % ("chi2",
spin135S.chi2, spin135F.chi2, spin137S.chi2, spin137F.chi2))
- self.assertAlmostEqual(spin135S.r2[0], 0, 4)
- self.assertAlmostEqual(spin135S.r2[1], 0, 4)
- self.assertAlmostEqual(spin135S.pA, 0, 4)
- self.assertAlmostEqual(spin135S.dw, 0, 4)
- self.assertAlmostEqual(spin135S.dwH, 0, 4)
- self.assertAlmostEqual(spin135S.kex/10000, 0, 4)
- self.assertAlmostEqual(spin135S.chi2, 0, 4)
- self.assertAlmostEqual(spin135F.r2[0], 0, 4)
- self.assertAlmostEqual(spin135F.r2[1], 0, 4)
- self.assertAlmostEqual(spin135F.pA, 0, 4)
- self.assertAlmostEqual(spin135F.dw, 0, 4)
- self.assertAlmostEqual(spin135F.dwH, 0, 4)
- self.assertAlmostEqual(spin135F.kex/10000, 0, 4)
- self.assertAlmostEqual(spin135F.chi2, 0, 4)
- self.assertAlmostEqual(spin137S.r2[0], 0, 4)
- self.assertAlmostEqual(spin137S.r2[1], 0, 4)
- self.assertAlmostEqual(spin137S.pA, 0, 4)
- self.assertAlmostEqual(spin137S.dw, 0, 4)
- self.assertAlmostEqual(spin137S.dwH, 0, 4)
- self.assertAlmostEqual(spin137S.kex/10000, 0, 4)
- self.assertAlmostEqual(spin137S.chi2, 0, 4)
- self.assertAlmostEqual(spin137F.r2[0], 0, 4)
- self.assertAlmostEqual(spin137F.r2[1], 0, 4)
- self.assertAlmostEqual(spin137F.pA, 0, 4)
- self.assertAlmostEqual(spin137F.dw, 0, 4)
- self.assertAlmostEqual(spin137F.dwH, 0, 4)
- self.assertAlmostEqual(spin137F.kex/10000, 0, 4)
- self.assertAlmostEqual(spin137F.chi2, 0, 4)
+
+ # Checks for residue :135S.
+ self.assertAlmostEqual(spin135S.r2[0], 2.89494989792968, 4)
+ self.assertAlmostEqual(spin135S.r2[1], 12.6694205621436, 4)
+ self.assertAlmostEqual(spin135S.pA, 0.500311298403094, 4)
+ self.assertAlmostEqual(spin135S.dw, 1.47777783753308, 4)
+ self.assertAlmostEqual(spin135S.dwH, 1.0880818550171, 4)
+ self.assertAlmostEqual(spin135S.kex, 59.5551680542025, 4)
+ self.assertAlmostEqual(spin135S.chi2, 347.259150126813, 4)
+
+ # Checks for residue :135F.
+ self.assertAlmostEqual(spin135F.r2[0], 41.907752972063, 4)
+ self.assertAlmostEqual(spin135F.r2[1], 58.1518607839796, 4)
+ self.assertAlmostEqual(spin135F.pA, 0.500311298403094, 4)
+ self.assertAlmostEqual(spin135F.dw, 0.419799242782033, 4)
+ self.assertAlmostEqual(spin135F.dwH, 1.27742823131436, 4)
+ self.assertAlmostEqual(spin135F.kex, 59.5551680542025, 4)
+ self.assertAlmostEqual(spin135F.chi2, 347.259150126813, 4)
+
+ # Checks for residue :137S.
+ self.assertAlmostEqual(spin137S.r2[0], 0.0736711146623223, 4)
+ self.assertAlmostEqual(spin137S.r2[1], 13.8168225329927, 4)
+ self.assertAlmostEqual(spin137S.pA, 0.500311298403094, 4)
+ self.assertAlmostEqual(spin137S.dw, 2.4030348485243, 4)
+ self.assertAlmostEqual(spin137S.dwH, 0.00285577518213064, 4)
+ self.assertAlmostEqual(spin137S.kex, 59.5551680542025, 4)
+ self.assertAlmostEqual(spin137S.chi2, 347.259150126813, 4)
+
+ # Checks for residue :137F.
+ self.assertAlmostEqual(spin137F.r2[0], 45.2885284912096, 4)
+ self.assertAlmostEqual(spin137F.r2[1], 57.8347181561312, 4)
+ self.assertAlmostEqual(spin137F.pA, 0.500311298403094, 4)
+ self.assertAlmostEqual(spin137F.dw, 1.5929498838754, 4)
+ self.assertAlmostEqual(spin137F.dwH, 0.00605967407110987, 4)
+ self.assertAlmostEqual(spin137F.kex, 59.5551680542025, 4)
+ self.assertAlmostEqual(spin137F.chi2, 347.259150126813, 4)
def test_tp02_data_to_ns_r1rho_2site(self, model=None):
r21121 - /branches/relax_disp/test_suite/system_tests/relax_disp.py