Author: tlinnet
Date: Tue Jun 17 09:33:32 2014
New Revision: 24013
URL: http://svn.gna.org/viewcvs/relax?rev=24013&view=rev
Log:
Temporary added systemtest: test_korzhnev_2005_all_data_disp_speed_bug.
This makes a minimisation with 1 iteration, and so will give the chi2 value
at the preset
parameter values.
This is chi2 value should give 162.5, but gives 74.7104.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24013&r1=24012&r2=24013&view=diff
==============================================================================
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py Tue
Jun 17 09:33:32 2014
@@ -3558,6 +3558,101 @@
self.assertAlmostEqual(spin.chi2/1000, 162.511988511609/1000, 3)
+ def test_korzhnev_2005_all_data_disp_speed_bug(self):
+ """Optimisation of all the Korzhnev et al., 2005 CPMG data using the
'NS MMQ 2-site' model.
+
+ This uses the data from Dmitry Korzhnev's paper at U{DOI:
10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}. This is the 1H SQ,
15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain
mutant.
+
+ Here all data will be optimised. The values found by cpmg_fit using
just this data are:
+
+ - r2 = {'H-S 500': 6.671649051677150, 'H-S 600':
6.988634195648529, 'H-S 800': 5.527971316790596,
+ 'N-S 500': 8.394988400015988, 'N-S 600':
8.891359568401835, 'N-S 800': 10.405356669006709,
+ 'NHZ 500': 5.936446687394352, 'NHZ 600':
6.717058062814535, 'NHZ 800': 6.838733853403030,
+ 'NHD 500': 8.593136215779710, 'NHD 600':
10.651511259239674, 'NHD 800': 12.567902357560627,
+ 'HNM 500': 7.851325614877817, 'HNM 600':
8.408803624020202, 'HNM 800': 11.227489645758979,
+ 'NHM 500': 9.189159145380575, 'NHM 600':
9.856814478405868, 'NHM 800': 11.967910041807118},
+ - pA = 0.943125351763911,
+ - dw = 4.421827493809807,
+ - dwH = -0.272637034755752,
+ - kex = 360.609744568697238,
+ - chi2 = 162.589570340050813.
+ """
+
+ # Base data setup.
+ self.setup_korzhnev_2005_data(data_list=['SQ', '1H SQ', 'DQ', 'ZQ',
'MQ', '1H MQ'])
+
+ # Alias the spin.
+ spin = return_spin(":9@N")
+
+ # The R20 keys.
+ r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=500e6)
+ r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=600e6)
+ r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=800e6)
+ r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
+ r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
+ r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
+ r20_key7 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
+ r20_key8 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
+ r20_key9 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
+ r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
+ r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
+ r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
+ r20_key13 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ,
frq=500e6)
+ r20_key14 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ,
frq=600e6)
+ r20_key15 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ,
frq=800e6)
+ r20_key16 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
+ r20_key17 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6)
+ r20_key18 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6)
+
+ # Set the initial parameter values.
+ spin.r2 = {
+ r20_key1: 6.67288025927458, r20_key2: 6.98951408255098,
r20_key3: 5.52959273852704,
+ r20_key4: 8.39471048876782, r20_key5: 8.89290699178799,
r20_key6: 10.40770687236930,
+ r20_key7: 5.93611174376373, r20_key8: 6.71735669582514,
r20_key9: 6.83835225518265,
+ r20_key10: 8.59615074668922, r20_key11: 10.65121378892910,
r20_key12: 12.57108229191090,
+ r20_key13: 7.85956711501608, r20_key14: 8.41891642907918,
r20_key15: 11.23620892230380,
+ r20_key16: 9.19654863789350, r20_key17: 9.86031627358462,
r20_key18: 11.97523755925750
+ }
+ spin.pA = 0.943129019477673
+ spin.dw = 4.42209952545181
+ spin.dwH = -0.27258970590969
+ spin.kex = 360.516132791038
+
+ # Low precision optimisation.
+ #self.interpreter.grid_search(lower=None, upper=None, inc=10,
constraints=True, verbosity=1)
+ self.interpreter.minimise(min_algor='simplex', func_tol=1e-05,
max_iter=1)
+
+ # Printout.
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s" % ("Parameter", "Value (:9)"))
+ print("%-20s %20.15g" % ("R2 (1H SQ - 500 MHz)", spin.r2[r20_key1]))
+ print("%-20s %20.15g" % ("R2 (1H SQ - 600 MHz)", spin.r2[r20_key2]))
+ print("%-20s %20.15g" % ("R2 (1H SQ - 800 MHz)", spin.r2[r20_key3]))
+ print("%-20s %20.15g" % ("R2 (SQ - 500 MHz)", spin.r2[r20_key4]))
+ print("%-20s %20.15g" % ("R2 (SQ - 600 MHz)", spin.r2[r20_key5]))
+ print("%-20s %20.15g" % ("R2 (SQ - 800 MHz)", spin.r2[r20_key6]))
+ print("%-20s %20.15g" % ("R2 (ZQ - 500 MHz)", spin.r2[r20_key7]))
+ print("%-20s %20.15g" % ("R2 (ZQ - 600 MHz)", spin.r2[r20_key8]))
+ print("%-20s %20.15g" % ("R2 (ZQ - 800 MHz)", spin.r2[r20_key9]))
+ print("%-20s %20.15g" % ("R2 (DQ - 500 MHz)", spin.r2[r20_key10]))
+ print("%-20s %20.15g" % ("R2 (DQ - 600 MHz)", spin.r2[r20_key11]))
+ print("%-20s %20.15g" % ("R2 (DQ - 800 MHz)", spin.r2[r20_key12]))
+ print("%-20s %20.15g" % ("R2 (1H MQ - 500 MHz)", spin.r2[r20_key13]))
+ print("%-20s %20.15g" % ("R2 (1H MQ - 600 MHz)", spin.r2[r20_key14]))
+ print("%-20s %20.15g" % ("R2 (1H MQ - 800 MHz)", spin.r2[r20_key15]))
+ print("%-20s %20.15g" % ("R2 (MQ - 500 MHz)", spin.r2[r20_key16]))
+ print("%-20s %20.15g" % ("R2 (MQ - 600 MHz)", spin.r2[r20_key17]))
+ print("%-20s %20.15g" % ("R2 (MQ - 800 MHz)", spin.r2[r20_key18]))
+ print("%-20s %20.15g" % ("pA", spin.pA))
+ print("%-20s %20.15g" % ("dw", spin.dw))
+ print("%-20s %20.15g" % ("dwH", spin.dwH))
+ print("%-20s %20.15g" % ("kex", spin.kex))
+ print("%-20s %20.15g\n" % ("chi2", spin.chi2))
+
+ # Checks for residue :9.
+ self.assertAlmostEqual(spin.chi2, 162.511988511609, 3)
+
+
def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72(self):
"""Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke
2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.
r24013 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py