Author: bugman
Date: Thu Nov 21 10:34:26 2013
New Revision: 21570
URL: http://svn.gna.org/viewcvs/relax?rev=21570&view=rev
Log:
Created the Relax_disp.test_korzhnev_2005_all_data system test for checking
the 'MMQ 2-site' model.
This checks against all six data types, 1H SQ, 15N SQ, DQ, ZQ, 1H MQ, and 15N
MQ. This is currently
set to the values found by cpmg_fit. As this is the true solution, relax
should find similar
parameter values.
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=21570&r1=21569&r2=21570&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Thu Nov 21
10:34:26 2013
@@ -1856,6 +1856,135 @@
self.assertAlmostEqual(spin.chi2, 50.32297, 4)
+ def test_korzhnev_2005_all_data(self):
+ """Optimisation of all the Korzhnev et al., 2005 CPMG data using the
'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': 6.778902, 'H-S 600': 7.097458, 'H-S 800':
5.635893,
+ 'N-S 500': 8.481132, 'N-S 600': 8.977845, 'N-S 800':
10.490257,
+ 'NHD 500': 8.693570, 'NHD 600': 10.744672, 'NHD 800':
12.647869,
+ 'NHZ 500': 6.043942, 'NHZ 600': 6.827802, 'NHZ 800':
6.946693,
+ 'NHM 500': 9.245925, 'NHM 600': 9.949255, 'NHM 800':
12.053031,
+ 'HNM 500': 7.887264, 'HNM 600': 8.506481, 'HNM 800':
11.276893},
+ - pA = 0.944322,
+ - kex = 368.075,
+ - dw = 4.413451,
+ - dwH = -0.271799,
+ - chi2 = 162.37981.
+ """
+
+ # 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_DQ, frq=500e6)
+ r20_key8 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
+ r20_key9 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
+ r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
+ r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
+ r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, 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: 6.778902, r20_key2: 7.097458, r20_key3: 5.635893,
+ r20_key4: 8.481132, r20_key5: 8.977845, r20_key6: 10.490257,
+ r20_key7: 8.693570, r20_key8: 10.744672, r20_key9: 12.647869,
+ r20_key10: 6.043942, r20_key11: 6.827802, r20_key12: 6.946693,
+ r20_key13: 9.245925, r20_key14: 9.949255, r20_key15: 12.053031,
+ r20_key16: 7.887264, r20_key17: 8.506481, r20_key18: 11.276893
+ }
+ spin.pA = 0.944322
+ spin.kex = 368.075
+ spin.dw = 4.413451
+ spin.dwH = -0.271799
+
+ # Low precision optimisation.
+ self.interpreter.minimise(min_algor='simplex', func_tol=1e-05,
max_iter=1000)
+
+ # Monte Carlo simulations.
+ self.interpreter.monte_carlo.setup(number=2)
+ self.interpreter.monte_carlo.create_data(method='back_calc')
+ self.interpreter.monte_carlo.initial_values()
+ self.interpreter.minimise(min_algor='simplex', max_iter=10)
+ self.interpreter.monte_carlo.error_analysis()
+
+ # Plot the dispersion curves.
+ self.interpreter.relax_disp.plot_disp_curves(dir='.', force=True)
+
+ # Save the results.
+ self.interpreter.state.save('state', dir='.', compress_type=1,
force=True)
+
+ # Printout.
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s" % ("Parameter", "Value (:9)"))
+ print("%-20s %20.15g" % ("R2 (SQ - 500 MHz)", spin.r2[r20_key1]))
+ print("%-20s %20.15g" % ("R2 (SQ - 600 MHz)", spin.r2[r20_key2]))
+ print("%-20s %20.15g" % ("R2 (SQ - 800 MHz)", spin.r2[r20_key3]))
+ print("%-20s %20.15g" % ("R2 (1H SQ - 500 MHz)", spin.r2[r20_key4]))
+ print("%-20s %20.15g" % ("R2 (1H SQ - 600 MHz)", spin.r2[r20_key5]))
+ print("%-20s %20.15g" % ("R2 (1H SQ - 800 MHz)", spin.r2[r20_key6]))
+ print("%-20s %20.15g" % ("R2 (DQ - 500 MHz)", spin.r2[r20_key7]))
+ print("%-20s %20.15g" % ("R2 (DQ - 600 MHz)", spin.r2[r20_key8]))
+ print("%-20s %20.15g" % ("R2 (DQ - 800 MHz)", spin.r2[r20_key9]))
+ print("%-20s %20.15g" % ("R2 (ZQ - 500 MHz)", spin.r2[r20_key10]))
+ print("%-20s %20.15g" % ("R2 (ZQ - 600 MHz)", spin.r2[r20_key11]))
+ print("%-20s %20.15g" % ("R2 (ZQ - 800 MHz)", spin.r2[r20_key12]))
+ print("%-20s %20.15g" % ("R2 (MQ - 500 MHz)", spin.r2[r20_key13]))
+ print("%-20s %20.15g" % ("R2 (MQ - 600 MHz)", spin.r2[r20_key14]))
+ print("%-20s %20.15g" % ("R2 (MQ - 800 MHz)", spin.r2[r20_key15]))
+ print("%-20s %20.15g" % ("R2 (1H MQ - 500 MHz)", spin.r2[r20_key16]))
+ print("%-20s %20.15g" % ("R2 (1H MQ - 600 MHz)", spin.r2[r20_key17]))
+ print("%-20s %20.15g" % ("R2 (1H 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.r2[r20_key1], 8.481132, 4)
+ self.assertAlmostEqual(spin.r2[r20_key2], 8.977845, 4)
+ self.assertAlmostEqual(spin.r2[r20_key3], 10.490257, 4)
+ self.assertAlmostEqual(spin.r2[r20_key4], 6.778902, 4)
+ self.assertAlmostEqual(spin.r2[r20_key5], 7.097458, 4)
+ self.assertAlmostEqual(spin.r2[r20_key6], 5.635893, 4)
+ self.assertAlmostEqual(spin.r2[r20_key7], 8.693570, 4)
+ self.assertAlmostEqual(spin.r2[r20_key8], 10.744672, 4)
+ self.assertAlmostEqual(spin.r2[r20_key9], 12.647869, 4)
+ self.assertAlmostEqual(spin.r2[r20_key10], 6.043942, 4)
+ self.assertAlmostEqual(spin.r2[r20_key11], 6.827802, 4)
+ self.assertAlmostEqual(spin.r2[r20_key12], 6.946693, 4)
+ self.assertAlmostEqual(spin.r2[r20_key13], 9.245925, 4)
+ self.assertAlmostEqual(spin.r2[r20_key14], 9.949255, 4)
+ self.assertAlmostEqual(spin.r2[r20_key15], 12.053031, 4)
+ self.assertAlmostEqual(spin.r2[r20_key16], 7.887264, 4)
+ self.assertAlmostEqual(spin.r2[r20_key17], 8.506481, 4)
+ self.assertAlmostEqual(spin.r2[r20_key18], 11.276893, 4)
+ self.assertAlmostEqual(spin.pA, 0.944322, 4)
+ self.assertAlmostEqual(spin.dw, 4.413451, 4)
+ self.assertAlmostEqual(spin.dwH, -0.271799, 4)
+ self.assertAlmostEqual(spin.kex/1000, 368.075/1000, 4)
+ self.assertAlmostEqual(spin.chi2, 162.37981, 4)
+
+
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.
r21570 - /branches/relax_disp/test_suite/system_tests/relax_disp.py