Author: bugman
Date: Tue Nov 19 08:35:24 2013
New Revision: 21511
URL: http://svn.gna.org/viewcvs/relax?rev=21511&view=rev
Log:
Created the Relax_disp.test_korzhnev_2005_15N_sq_data system test.
This is used to check the optimisation of the 15N SQ CPMG data using the 'MMQ
2-site' model.
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=21511&r1=21510&r2=21511&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Tue Nov 19
08:35:24 2013
@@ -30,7 +30,7 @@
import dep_check
from pipe_control.mol_res_spin import return_spin, spin_loop
from specific_analyses.relax_disp.disp_data import generate_r20_key,
get_curve_type
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_MQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99,
MODEL_LIST_CPMG, MODEL_LM63, MODEL_M61B, MODEL_NOREX,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_R2EFF
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_MQ,
EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_R1RHO, 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.clean_up import deletion
from test_suite.system_tests.base_classes import SystemTestCase
@@ -132,6 +132,75 @@
# Copy the data.
self.interpreter.value.copy(pipe_from='R2eff', pipe_to=model,
param='r2eff')
+
+
+ def setup_korzhnev_2005_data(self, data_list=[]):
+ """Set up the data for the test_korzhnev_2005_data_*() system tests
using the 'MMQ 2-site' model.
+
+ This loads the proton-heteronuclear SQ, ZQ, DQ, and MQ (MMQ) data
from:
+
+ - Dmitry M. Korzhnev, Philipp Neudecker, Anthony Mittermaier,
Vladislav Yu. Orekhov, and Lewis E. Kay (2005) Multiple-site exchange in
proteins studied with a suite of six
+NMR relaxation dispersion experiments: An application to the folding of a
Fyn SH3 domain mutant. 127, 15602-15611 (U{DOI:
10.1021/ja054550e<http://dx.doi.org/10.1021/ja054550e>}).
+
+ It consists of the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for
residue Asp 9 of the Fyn SH3 domain mutant.
+
+
+ @keyword data_list: The list of data to load. It can contain 'SQ',
'1H SQ', 'ZQ', 'DQ', 'MQ', and '1H MQ'.
+ @type data_list: list of str
+ """
+
+ # Create the data pipe and load the base data.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Korzhnev_et_al_2005'
+ self.interpreter.pipe.create(pipe_name='Korzhnev et al., 2005',
pipe_type='relax_disp')
+
+ # Create the spin system.
+ self.interpreter.spin.create(res_name='Asp', res_num=9,
spin_name='N')
+ self.interpreter.spin.element('N', spin_id='@N')
+ self.interpreter.spin.isotope('15N', spin_id='@N')
+
+ # The spectral data - experiment ID, R2eff file name, experiment
type, spin ID string, spectrometer frequency in Hertz, relaxation time.
+ data = [
+ ['1H SQ', '1H_CPMG_500_MHz', 'hs_500.res',
EXP_TYPE_CPMG_PROTON_SQ, ':9@H', 500e6, 0.03],
+ ['1H SQ', '1H_CPMG_600_MHz', 'hs_600.res',
EXP_TYPE_CPMG_PROTON_SQ, ':9@H', 600e6, 0.03],
+ ['1H SQ', '1H_CPMG_800_MHz', 'hs_800.res',
EXP_TYPE_CPMG_PROTON_SQ, ':9@H', 800e6, 0.03],
+ ['SQ', '15N_CPMG_500_MHz', 'ns_500.res', EXP_TYPE_CPMG_SQ,
':9@N', 500e6, 0.04],
+ ['SQ', '15N_CPMG_600_MHz', 'ns_600.res', EXP_TYPE_CPMG_SQ,
':9@N', 600e6, 0.04],
+ ['SQ', '15N_CPMG_800_MHz', 'ns_800.res', EXP_TYPE_CPMG_SQ,
':9@N', 800e6, 0.04]
+ ]
+ cpmg_frqs_1h_sq = [67.0, 133.0, 267.0, 400.0, 533.0, 667.0, 800.0,
933.0, 1067.0, 1600.0, 2133.0, 2667.0]
+ cpmg_frqs_sq = [50.0, 100.0, 150.0, 200.0, 250.0, 300.0, 350.0,
400.0, 450.0, 500.0, 600.0, 700.0, 800.0, 900.0, 1000.0]
+
+ # Loop over the files, reading in the data.
+ for data_type, id, file, exp_type, spin_id, H_frq, relax_time in
data:
+ # Skip undesired data.
+ if data_type not in data_list:
+ continue
+
+ # Alias the CPMG frequencies.
+ if data_type == 'SQ':
+ cpmg_frqs = cpmg_frqs_sq
+ elif data_type == '1H SQ':
+ cpmg_frqs = cpmg_frqs_1h_sq
+
+ # Loop over each CPMG frequency.
+ for cpmg_frq in cpmg_frqs:
+ # The id.
+ new_id = "%s_%s" % (id, cpmg_frq)
+
+ # Set the NMR field strength.
+ self.interpreter.spectrometer.frequency(id=new_id, frq=H_frq)
+
+ # Set the relaxation dispersion experiment type.
+ self.interpreter.relax_disp.exp_type(spectrum_id=new_id,
exp_type=exp_type)
+
+ # Relaxation dispersion CPMG constant time delay T (in s).
+ self.interpreter.relax_disp.relax_time(spectrum_id=new_id,
time=relax_time)
+
+ # Read the R2eff data.
+ self.interpreter.relax_disp.r2eff_read_spin(id=id, file=file,
dir=data_path, spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)
+
+ # Change the model.
+ self.interpreter.relax_disp.select_model('MMQ 2-site')
def test_bug_21081_disp_cluster_fail(self):
@@ -1329,6 +1398,74 @@
self.assertEqual(spin2[i], lines[i])
+ def test_korzhnev_2005_15N_sq_data(self):
+ """Optimisation of the Korzhnev et al., 2005 15N SQ 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 only the 15N SQ data will be optimised. The values found by
cpmg_fit using just this data are:
+
+ - r2 = {'500': 8.400699, '600': 8.847946, '800': 10.289079},
+ - pA = 0.950701,
+ - kex = 435.592,
+ - dw = 4.356895,
+ - chi2 = 17.49720.
+ """
+
+ # Base data setup.
+ self.setup_korzhnev_2005_data(data_list=['SQ'])
+
+ # Alias the spin.
+ spin = return_spin(":9")
+
+ # The R20 keys.
+ r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
+ r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
+ r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
+
+ # Set the initial parameter values.
+ spin.r2 = {r20_key1: 8.334232330326190, r20_key2: 8.756773997879968,
r20_key3: 10.219320492033058}
+ spin.pA = 0.950310172115387
+ spin.kex = 433.176323890829849
+ spin.dw = 4.356737157889636
+
+ # 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=ds.tmpdir,
force=True)
+
+ # Save the results.
+ self.interpreter.state.save('state', dir=ds.tmpdir, compress_type=1,
force=True)
+
+ # Printout.
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s" % ("Parameter", "Value (:9)"))
+ print("%-20s %20.15g" % ("R2 (500 MHz)", spin.r2[r20_key1]))
+ print("%-20s %20.15g" % ("R2 (600 MHz)", spin.r2[r20_key2]))
+ print("%-20s %20.15g" % ("R2 (800 MHz)", spin.r2[r20_key3]))
+ print("%-20s %20.15g" % ("pA", spin.pA))
+ print("%-20s %20.15g" % ("dw", spin.dw))
+ 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], 8.334232330326190, 4)
+ self.assertAlmostEqual(spin.r2[r20_key2], 8.756773997879968, 4)
+ self.assertAlmostEqual(spin.r2[r20_key3], 10.219320492033058, 4)
+ self.assertAlmostEqual(spin.pA, 0.950310172115387, 4)
+ self.assertAlmostEqual(spin.dw, 4.356737157889636, 4)
+ self.assertAlmostEqual(spin.kex/1000, 433.176323890829849/1000, 4)
+ self.assertAlmostEqual(spin.chi2, 17.37460582872912, 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.
r21511 - /branches/relax_disp/test_suite/system_tests/relax_disp.py