Author: bugman
Date: Wed Jul 17 20:08:17 2013
New Revision: 20378
URL: http://svn.gna.org/viewcvs/relax?rev=20378&view=rev
Log:
Created system tests for the rest of the numerical dispersion models.
These include Relax_disp.test_hansen_cpmg_data_ns_2site_expanded,
Relax_disp.test_hansen_cpmg_data_ns_2site_star and
Relax_disp.test_hansen_cpmg_data_ns_2site_star_full.
This checks the 'NS 2-site expanded', 'NS 2-site star', and 'NS 2-site star
full' numerical
dispersion models against some truncated CPMG data from Flemming Hansen. The
parameter checks have
not been updated for the 'NS 2-site expanded' and 'NS 2-site star full'
models as there appears to
be bugs.
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=20378&r1=20377&r2=20378&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Wed Jul 17
20:08:17 2013
@@ -434,6 +434,169 @@
# Base data setup.
self.setup_hansen_cpmg_data(model='NS 2-site 3D full')
+
+ # Alias the spins.
+ spin70 = cdp.mol[0].res[0].spin[0]
+ spin71 = cdp.mol[0].res[1].spin[0]
+
+ # Set the initial parameter values.
+ spin70.r2a = [6.994165925, 9.428129427]
+ spin70.r2b = [6.994165925, 9.428129427]
+ spin70.pA = 0.9897754407
+ spin70.dw = 5.642418428
+ spin70.kex = 1743.666375
+ spin71.r2a = [4.978654237, 9.276918959]
+ spin71.r2b = [4.978654237, 9.276918959]
+ spin71.pA = 0.9968032899
+ spin71.dw = 4.577891393
+ spin71.kex = 1830.044597
+
+ # 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=1000, constraints=False, scaling=True, verbosity=1)
+
+ # Printout.
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value
(:71)"))
+ print("%-20s %20.15g %20.15g" % ("R2A (500 MHz)", spin70.r2a[0],
spin71.r2a[0]))
+ print("%-20s %20.15g %20.15g" % ("R2B (500 MHz)", spin70.r2b[0],
spin71.r2b[0]))
+ print("%-20s %20.15g %20.15g" % ("R2A (800 MHz)", spin70.r2a[1],
spin71.r2a[1]))
+ print("%-20s %20.15g %20.15g" % ("R2B (800 MHz)", spin70.r2b[1],
spin71.r2b[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))
+
+ # Checks for residue :70.
+ self.assertAlmostEqual(spin70.r2a[0], 6.99588673577837, 4)
+ self.assertAlmostEqual(spin70.r2b[0], 9.45248596611036, 4)
+ self.assertAlmostEqual(spin70.r2a[1], 6.99588673577837, 4)
+ self.assertAlmostEqual(spin70.r2b[1], 9.45248596611036, 4)
+ self.assertAlmostEqual(spin70.pA, 0.989751958251912, 4)
+ self.assertAlmostEqual(spin70.dw, 5.64481346432097, 4)
+ self.assertAlmostEqual(spin70.kex/1000, 1723.62510048637/1000, 4)
+ self.assertAlmostEqual(spin70.chi2, 18.0983759853235, 4)
+
+ # Checks for residue :71.
+ self.assertAlmostEqual(spin71.r2a[0], 4.97891921568573, 4)
+ self.assertAlmostEqual(spin71.r2b[0], 4.97891921568573, 4)
+ self.assertAlmostEqual(spin71.pA, 0.996807857237692, 4)
+ self.assertAlmostEqual(spin71.dw, 4.58200738669362, 4)
+ self.assertAlmostEqual(spin71.kex/1000, 1821.36206334352/1000, 4)
+ self.assertAlmostEqual(spin71.chi2, 1.37073030640607, 4)
+
+
+ def test_hansen_cpmg_data_ns_2site_expanded(self):
+ """Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS 2-site
expanded' dispersion model.
+
+ 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.
+ """
+
+ # Base data setup.
+ self.setup_hansen_cpmg_data(model='NS 2-site expanded')
+
+ # Alias the spins.
+ spin70 = cdp.mol[0].res[0].spin[0]
+ spin71 = cdp.mol[0].res[1].spin[0]
+
+ # Set the initial parameter values.
+ spin70.r2 = [6.994165925, 9.428129427]
+ spin70.pA = 0.9897754407
+ spin70.dw = 5.642418428
+ spin70.kex = 1743.666375
+ spin71.r2 = [4.978654237, 9.276918959]
+ spin71.pA = 0.9968032899
+ spin71.dw = 4.577891393
+ spin71.kex = 1830.044597
+
+ # 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=1000, constraints=False, scaling=True, verbosity=1)
+
+ # Printout.
+ 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))
+
+ # Checks for residue :70.
+ self.assertAlmostEqual(spin70.r2[0], 6.99588673577837, 4)
+ self.assertAlmostEqual(spin70.r2[1], 9.45248596611036, 4)
+ self.assertAlmostEqual(spin70.pA, 0.989751958251912, 4)
+ self.assertAlmostEqual(spin70.dw, 5.64481346432097, 4)
+ self.assertAlmostEqual(spin70.kex/1000, 1723.62510048637/1000, 4)
+ self.assertAlmostEqual(spin70.chi2, 18.0983759853235, 4)
+
+ # Checks for residue :71.
+ self.assertAlmostEqual(spin71.r2[0], 4.97891921568573, 4)
+ self.assertAlmostEqual(spin71.pA, 0.996807857237692, 4)
+ self.assertAlmostEqual(spin71.dw, 4.58200738669362, 4)
+ self.assertAlmostEqual(spin71.kex/1000, 1821.36206334352/1000, 4)
+ self.assertAlmostEqual(spin71.chi2, 1.37073030640607, 4)
+
+
+ def test_hansen_cpmg_data_ns_2site_star(self):
+ """Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS 2-site
star' dispersion model.
+
+ 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.
+ """
+
+ # Base data setup.
+ self.setup_hansen_cpmg_data(model='NS 2-site star')
+
+ # Alias the spins.
+ spin70 = cdp.mol[0].res[0].spin[0]
+ spin71 = cdp.mol[0].res[1].spin[0]
+
+ # Set the initial parameter values.
+ spin70.r2 = [6.996327746, 9.452051268]
+ spin70.pA = 0.9897519798
+ spin70.dw = 5.644862195
+ spin70.kex = 1723.820567
+ spin71.r2 = [4.978654237, 9.276918959]
+ spin71.pA = 0.9968032899
+ spin71.dw = 4.577891393
+ spin71.kex = 1830.044597
+
+ # 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=1000, constraints=False, scaling=True, verbosity=1)
+
+ # Printout.
+ 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))
+
+ # Checks for residue :70.
+ self.assertAlmostEqual(spin70.r2[0], 6.99632787205716, 4)
+ self.assertAlmostEqual(spin70.r2[1], 9.4520515321858, 4)
+ self.assertAlmostEqual(spin70.pA, 0.989751979646436, 4)
+ self.assertAlmostEqual(spin70.dw, 5.64486197944831, 4)
+ self.assertAlmostEqual(spin70.kex/1000, 1723.82057518556/1000, 4)
+ self.assertAlmostEqual(spin70.chi2, 18.0982961523327, 4)
+
+ # Checks for residue :71.
+ self.assertAlmostEqual(spin71.r2[0], 4.97869498800177, 4)
+ self.assertAlmostEqual(spin71.pA, 0.996808845898761, 4)
+ self.assertAlmostEqual(spin71.dw, 4.58279535811262, 4)
+ self.assertAlmostEqual(spin71.kex/1000, 1822.71231082936/1000, 4)
+ self.assertAlmostEqual(spin71.chi2, 1.37073226641439, 4)
+
+
+ def test_hansen_cpmg_data_ns_2site_star_full(self):
+ """Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS 2-site
star full' dispersion model.
+
+ 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.
+ """
+
+ # Base data setup.
+ self.setup_hansen_cpmg_data(model='NS 2-site star full')
# Alias the spins.
spin70 = cdp.mol[0].res[0].spin[0]
r20378 - /branches/relax_disp/test_suite/system_tests/relax_disp.py