Class Relax_disp

Class for testing various aspects specific to relaxation dispersion curve-fitting.

Nested Classes

Inherited from unittest.case.TestCase: failureException

Instance Methods

__init__(self, methodName='runTest')
Skip certain tests if the C modules are non-functional.

setUp(self)
Set up for all the functional tests.

setup_bug_22146_unpacking_r2a_r2b_cluster(self, folder=None, model_analyse=None, places=7)
Setup data for the catch of bug #22146, the failure of unpacking R2A and R2B, when performing a clustered full dispersion models.

setup_hansen_cpmg_data(self, model=None)
Set up the data for the test_hansen_cpmg_data_*() system tests.

setup_kteilum_fmpoulsen_makke_cpmg_data(self, model=None, expfolder=None)
Set up the data for the test_kteilum_fmpoulsen_makke_cpmg_data_*() system tests.

setup_korzhnev_2005_data(self, data_list=[])
Set up the data for the test_korzhnev_2005_data_*() system tests using the 'NS MMQ 2-site' model.

setup_sod1wt_t25(self, pipe_name, pipe_type, pipe_name_r2eff, select_spin_index)
Setup of data SOD1-WT CPMG.

test_baldwin_synthetic(self)
Test synthetic data of Andrew J.

test_baldwin_synthetic_full(self)
Test synthetic data of Andrew J.

test_bug_21081_disp_cluster_fail(self)
Bug #21081 catch, the failure of a cluster analysis when spins are deselected.

test_bug_21460_disp_cluster_fail(self)
Bug #21460 catch, the failure due to a spectrometer frequency having no relaxation data.

test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp(self)
Bug #21665 catch, the failure of an analysis of a sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths using auto_analysis.

test_bug_21665_cpmg_two_fields_two_delaytimes_fail_calc(self)
Bug #21665 catch, the failure due to a a CPMG analysis recorded at two fields at two delay times, using calc().

test_bug_21665_cpmg_two_fields_two_delaytimes_fail_relax_disp(self)
Bug #21665 catch, the failure due to a a CPMG analysis recorded at two fields at two delay times using auto_analysis.

test_bug_21715_clustered_indexerror(self)
Catch bug #21715, the failure of a clustered auto-analysis due to an IndexError.

test_bug_22146_unpacking_r2a_r2b_cluster_B14(self)
Catch bug #22146, the failure of unpacking R2A and R2B, when performing a clustered B14 full analysis.

test_bug_22146_unpacking_r2a_r2b_cluster_CR72(self)
Catch bug #22146, the failure of unpacking R2A and R2B, when performing a clustered CR72 full analysis.

test_bug_22146_unpacking_r2a_r2b_cluster_NS_3D(self)
Catch bug #22146, the failure of unpacking R2A and R2B, when performing a clustered NS CPMG 2SITE 3D full analysis.

test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR(self)
Catch bug #22146, the failure of unpacking R2A and R2B, when performing a clustered NS CPMG 2SITE STAR full analysis.

test_cpmg_synthetic_ns3d_to_cr72(self)
Test synthetic cpmg data.

test_cpmg_synthetic_ns3d_to_b14(self)
Test synthetic cpmg data.

test_cpmg_synthetic_ns3d_to_cr72_noise_cluster(self)
Test synthetic cpmg data.

test_cpmg_synthetic_dx_map_points(self)
Test synthetic cpmg data, calling the dx.map function with one or two points.

test_curve_type_cpmg_fixed_time(self)
Test the curve type detection using the Dr.

test_curve_type_r1rho_exponential(self, model=None)
Test the curve type detection using the 'M61' exponential test data.

test_curve_type_r1rho_fixed_time(self, model=None)
Test the curve type detection using the 'TP02' fixed time test data.

test_dpl94_data_to_dpl94(self)
Test the relaxation dispersion 'DPL94' model curve fitting to fixed time synthetic data.

test_exp_fit(self)
Test the relaxation dispersion 'exp_fit' model curve fitting.

test_hansen_catia_input(self)
Conversion of Dr.

test_hansen_cpmg_data_auto_analysis(self)
Test of the dispersion auto-analysis using Dr.

test_hansen_cpmg_data_auto_analysis_numeric(self)
Test of the numeric model only dispersion auto-analysis using Dr.

test_hansen_cpmg_data_auto_analysis_r2eff(self)
Test of the dispersion auto-analysis using Dr.

test_hansen_cpmg_data_missing_auto_analysis(self)
Test of the dispersion auto-analysis using Dr.

test_hansen_cpmg_data_to_cr72(self)
Optimisation of Dr.

test_hansen_cpmg_data_to_cr72_full(self)
Optimisation of Dr.

test_hansen_cpmg_data_to_it99(self)
Optimisation of Dr.

test_hansen_cpmg_data_to_lm63(self)
Optimisation of Dr.

test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self)
Optimisation of Dr.

test_hansen_cpmg_data_to_ns_cpmg_2site_3D_full(self)
Optimisation of Dr.

test_hansen_cpmg_data_to_ns_cpmg_2site_expanded(self)
Optimisation of Dr.

test_hansen_cpmg_data_to_ns_cpmg_2site_star(self)
Optimisation of Dr.

test_hansen_cpmg_data_to_ns_cpmg_2site_star_full(self)
Optimisation of Dr.

test_hansen_cpmgfit_input(self)
Conversion of Dr.

test_korzhnev_2005_15n_dq_data(self)
Optimisation of the Korzhnev et al., 2005 15N DQ CPMG data using the 'NS MMQ 2-site' model.

test_korzhnev_2005_15n_mq_data(self)
Optimisation of the Korzhnev et al., 2005 15N MQ CPMG data using the 'NS MMQ 2-site' model.

test_korzhnev_2005_15n_sq_data(self)
Optimisation of the Korzhnev et al., 2005 15N SQ CPMG data using the 'NS MMQ 2-site' model.

test_korzhnev_2005_15n_zq_data(self)
Optimisation of the Korzhnev et al., 2005 15N ZQ CPMG data using the 'NS MMQ 2-site' model.

test_korzhnev_2005_1h_mq_data(self)
Optimisation of the Korzhnev et al., 2005 1H MQ CPMG data using the 'NS MMQ 2-site' model.

test_korzhnev_2005_1h_sq_data(self)
Optimisation of the Korzhnev et al., 2005 1H SQ CPMG data using the 'NS MMQ 2-site' model.

test_korzhnev_2005_all_data(self)
Optimisation of all the Korzhnev et al., 2005 CPMG data using the 'NS MMQ 2-site' model.

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.

test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72_full(self)
Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.

test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_tsmfk01(self)
Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.

test_kteilum_fmpoulsen_makke_cpmg_data_101m_guhcl_to_tsmfk01(self)
Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.

test_lm63_3site_synthetic(self)
Test the 'LM63 3-site' dispersion model using the pure noise-free synthetic data.

test_m61_data_to_m61(self)
Test the relaxation dispersion 'M61' model curve fitting to fixed time synthetic data.

test_m61_exp_data_to_m61(self)
Test the relaxation dispersion 'M61' model curve fitting to the full exponential synthetic data.

xxx_test_m61b_data_to_m61b(self)
Test the relaxation dispersion 'M61 skew' model curve fitting to fixed time synthetic data.

test_ns_mmq_3site(self)
Compare the 'NS MMQ 3-site' dispersion model to synthetic data from cpmg_fit.

test_ns_mmq_3site_linear(self)
Compare the 'NS MMQ 3-site linear' dispersion model to synthetic data from cpmg_fit.

test_ns_r1rho_3site(self)
Compare the 'NS R1rho 3-site' dispersion model to synthetic data from cpmg_fit.

test_ns_r1rho_3site_linear(self)
Compare the 'NS R1rho 3-site linear' dispersion model to synthetic data from cpmg_fit.

test_r1rho_kjaergaard(self)
Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.

test_r2eff_read(self)
Test the operation of the relax_disp.r2eff_read user function.

test_r2eff_read_spin(self)
Test the operation of the relax_disp.r2eff_read_spin user function.

test_r2eff_fit_fixed_time(self)
Test the relaxation dispersion 'R2eff' model for fixed time data in the auto-analysis.

test_read_r2eff(self)
Test the reading of a file containing r2eff values.

test_r20_from_min_r2eff_cpmg(self)
Test speeding up grid search.

test_sod1wt_t25_bug_21954_order_error_analysis(self)
Error analysis of SOD1-WT CPMG.

test_sod1wt_t25_to_cr72(self)
Optimisation of SOD1-WT CPMG.

test_sod1wt_t25_to_sherekhan_input(self)
Conversion of SOD1-WT CPMG R2eff values into input files for sherekhan.

test_sprangers_data_to_mmq_cr72(self, model=None)
Test the 'MMQ CR72' model fitting against Remco Sprangers' ClpP data.

test_sprangers_data_to_ns_mmq_2site(self, model=None)
Test the 'NS MMQ 2-site' model fitting against Remco Sprangers' ClpP data.

test_tp02_data_to_ns_r1rho_2site(self, model=None)
Test the relaxation dispersion 'NS R1rho 2-site' model fitting against the 'TP02' test data.

test_tp02_data_to_mp05(self)
Test the dispersion 'MP05' model fitting against the 'TP02' test data.

test_tp02_data_to_tap03(self)
Test the dispersion 'TAP03' model fitting against the 'TP02' test data.

test_tp02_data_to_tp02(self)
Test the relaxation dispersion 'TP02' model curve fitting to fixed time synthetic data.

test_value_write_calc_rotating_frame_params_int(self)
System test of the value.write function to write intensities for an R1rho setup.

test_value_write_calc_rotating_frame_params_theta(self)
System test of the value.write function to write return values of theta from calc_rotating_frame_params() function for an R1rho setup.

test_value_write_calc_rotating_frame_params_w_eff(self)
System test of the value.write function to write return values of w_eff from calc_rotating_frame_params() function for an R1rho setup.

test_value_write_calc_rotating_frame_params_auto_analysis(self)
System test of the auto_analysis value.write function to write theta and w_eff values for an R1rho setup.

Inherited from base_classes.SystemTestCase: script_exec, tearDown

Inherited from unittest.case.TestCase: __call__, __eq__, __hash__, __ne__, __repr__, __str__, addCleanup, addTypeEqualityFunc, assertAlmostEqual, assertAlmostEquals, assertDictContainsSubset, assertDictEqual, assertEqual, assertEquals, assertFalse, assertGreater, assertGreaterEqual, assertIn, assertIs, assertIsInstance, assertIsNone, assertIsNot, assertIsNotNone, assertItemsEqual, assertLess, assertLessEqual, assertListEqual, assertMultiLineEqual, assertNotAlmostEqual, assertNotAlmostEquals, assertNotEqual, assertNotEquals, assertNotIn, assertNotIsInstance, assertNotRegexpMatches, assertRaises, assertRaisesRegexp, assertRegexpMatches, assertSequenceEqual, assertSetEqual, assertTrue, assertTupleEqual, assert_, countTestCases, debug, defaultTestResult, doCleanups, fail, failIf, failIfAlmostEqual, failIfEqual, failUnless, failUnlessAlmostEqual, failUnlessEqual, failUnlessRaises, id, run, shortDescription, skipTest

Inherited from unittest.case.TestCase (private): _addSkip, _baseAssertEqual, _deprecate, _formatMessage, _getAssertEqualityFunc, _truncateMessage

Inherited from object: __delattr__, __format__, __getattribute__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Class Methods

Inherited from unittest.case.TestCase: setUpClass, tearDownClass

Class Variables

Inherited from unittest.case.TestCase: longMessage, maxDiff

Inherited from unittest.case.TestCase (private): _classSetupFailed, _diffThreshold

Properties

Inherited from object: __class__

Method Details

__init__(self, methodName='runTest')
(Constructor)

Skip certain tests if the C modules are non-functional.

Parameters:

• methodName (str) - The name of the test.

Overrides: object.__init__

setUp(self)

Set up for all the functional tests.

Overrides: unittest.case.TestCase.setUp

setup_bug_22146_unpacking_r2a_r2b_cluster(self, folder=None, model_analyse=None, places=7)

Setup data for the catch of bug #22146, the failure of unpacking R2A and R2B, when performing a clustered full dispersion models.

Parameters:

• folder (str) - The name of the folder for the test data.
• model_analyse (str) - The name of the model which will be tested.

setup_hansen_cpmg_data(self, model=None)

Set up the data for the test_hansen_cpmg_data_*() system tests.

Parameters:

• model (str) - The name of the model which will be tested.

setup_kteilum_fmpoulsen_makke_cpmg_data(self, model=None, expfolder=None)

Set up the data for the test_kteilum_fmpoulsen_makke_cpmg_data_*() system tests.

Parameters:

• model (str) - The name of the model which will be tested.

setup_korzhnev_2005_data(self, data_list=[])

Set up the data for the test_korzhnev_2005_data_*() system tests using the 'NS 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 (DOI: 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.

Parameters:

• data_list (list of str) - The list of data to load. It can contain 'SQ', '1H SQ', 'ZQ', 'DQ', 'MQ', and '1H MQ'.

setup_sod1wt_t25(self, pipe_name, pipe_type, pipe_name_r2eff, select_spin_index)

Setup of data SOD1-WT CPMG. From paper at http://dx.doi.org/10.1073/pnas.0907387106.

Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius.

test_baldwin_synthetic(self)

Test synthetic data of Andrew J. Baldwin B14 model whereby the simplification R20A = R20B is assumed.

Support requst sr #3154 https://web.archive.org/web/https://gna.org/support/index.php?3154.

This uses the synthetic data from paper DOI: 10.1016/j.jmr.2014.02.023 with R20A, R20B = 2. rad/s.

test_baldwin_synthetic_full(self)

Test synthetic data of Andrew J. Baldwin B14 model. Support requst sr #3154 https://web.archive.org/web/https://gna.org/support/index.php?3154.

This uses the synthetic data from paper DOI: 10.1016/j.jmr.2014.02.023.

test_cpmg_synthetic_ns3d_to_cr72(self)

Test synthetic cpmg data.

This script will produce synthetic CPMG R2eff values according to the NS CPMG 2-site 3D model, and the fit the data with CR72.

test_cpmg_synthetic_ns3d_to_b14(self)

Test synthetic cpmg data.

This script will produce synthetic CPMG R2eff values according to the NS CPMG 2-site 3D model, and the fit the data with B14. Try to catch bug #22021 https://web.archive.org/web/https://gna.org/bugs/index.php?22021: Model B14 shows bad fitting to data.

test_cpmg_synthetic_ns3d_to_cr72_noise_cluster(self)

Test synthetic cpmg data. For CR72 with small noise and cluster.

This script will produce synthetic CPMG R2eff values according to the selected model, and the fit the selected model.

test_cpmg_synthetic_dx_map_points(self)

Test synthetic cpmg data, calling the dx.map function with one or two points.

This script will produce synthetic CPMG R2eff values according to the selected model, and the fit the selected model.

test_curve_type_cpmg_fixed_time(self)

Test the curve type detection using the Dr. Flemming Hansen's CPMG fixed time test data.

test_hansen_catia_input(self)

Conversion of Dr. Flemming Hansen's CPMG R2eff values into input files for CATIA.

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.

test_hansen_cpmg_data_auto_analysis(self)

Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data.

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.

test_hansen_cpmg_data_auto_analysis_numeric(self)

Test of the numeric model only dispersion auto-analysis using Dr. Flemming Hansen's CPMG data.

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.

test_hansen_cpmg_data_auto_analysis_r2eff(self)

Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data (using the R2eff data directly instead of peak intensities).

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.

test_hansen_cpmg_data_missing_auto_analysis(self)

Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data with parts missing.

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.

test_hansen_cpmg_data_to_cr72(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the CR72 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.

test_hansen_cpmg_data_to_cr72_full(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the CR72 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.

test_hansen_cpmg_data_to_it99(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the IT99 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.

test_hansen_cpmg_data_to_lm63(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the LM63 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.

test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site 3D' 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.

test_hansen_cpmg_data_to_ns_cpmg_2site_3D_full(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site 3D 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.

test_hansen_cpmg_data_to_ns_cpmg_2site_expanded(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 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.

test_hansen_cpmg_data_to_ns_cpmg_2site_star(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 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.

test_hansen_cpmg_data_to_ns_cpmg_2site_star_full(self)

Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 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.

test_hansen_cpmgfit_input(self)

Conversion of Dr. Flemming Hansen's CPMG R2eff values into input files for CPMGFit.

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.

test_korzhnev_2005_15n_dq_data(self)

Optimisation of the Korzhnev et al., 2005 15N DQ CPMG data using the 'NS MMQ 2-site' model.

This uses the data from Dmitry Korzhnev's paper at DOI: 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 DQ data will be optimised. The values found by cpmg_fit using just this data are:

• r2 = {'500': 9.487269007171426, '600': 11.718267257562591, '800': 13.624551743116887},
• pA = 0.965402506690231,
• dw = 0.805197170133360,
• dwH = -0.595536627771890,
• kex = 569.003663067619868,
• chi2 = 9.297671357952812.

test_korzhnev_2005_15n_mq_data(self)

Optimisation of the Korzhnev et al., 2005 15N MQ CPMG data using the 'NS MMQ 2-site' model.

This uses the data from Dmitry Korzhnev's paper at DOI: 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 MQ data will be optimised. The values found by cpmg_fit using just this data are:

• r2 = {'500': 5.993083514798655, '600': 6.622184438384841, '800': 8.640765919352019},
• pA = 0.930027999814003,
• dw = 4.338620619954370,
• dwH = -0.274250775560818,
• kex = 344.613362916544475,
• chi2 = 10.367733168217050.

test_korzhnev_2005_15n_sq_data(self)

Optimisation of the Korzhnev et al., 2005 15N SQ CPMG data using the 'NS MMQ 2-site' model.

This uses the data from Dmitry Korzhnev's paper at DOI: 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': 8.335037972570017, '600': 8.761366016417508, '800': 10.225001019091822},
• pA = 0.950003458294991,
• dw = 4.358402855315123,
• kex = 429.906473361926999,
• chi2 = 17.393331915567252.

test_korzhnev_2005_15n_zq_data(self)

Optimisation of the Korzhnev et al., 2005 15N ZQ CPMG data using the 'NS MMQ 2-site' model.

This uses the data from Dmitry Korzhnev's paper at DOI: 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 ZQ data will be optimised. The values found by cpmg_fit using just this data are:

• r2 = {'500': 5.909812628572937, '600': 6.663690132557320, '800': 6.787171647689906},
• pA = 0.942452612380140,
• dw = 0.858972784230892,
• dwH = 0.087155962730608,
• kex = 373.219151384798920,
• chi2 = 23.863208106025152.

test_korzhnev_2005_1h_mq_data(self)

Optimisation of the Korzhnev et al., 2005 1H MQ CPMG data using the 'NS MMQ 2-site' model.

This uses the data from Dmitry Korzhnev's paper at DOI: 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 1H MQ data will be optimised. The values found by cpmg_fit using just this data are:

• r2 = {'500': -0.000016676911302, '600': 0.036594127620440, '800': 2.131014839635728},
• pA = 0.936911090448340,
• dw = 4.325314846914845,
• dwH = -0.213870168665628,
• kex = 487.361914835074117,
• chi2 = 14.870371897291138.

test_korzhnev_2005_1h_sq_data(self)

Optimisation of the Korzhnev et al., 2005 1H SQ CPMG data using the 'NS MMQ 2-site' model.

This uses the data from Dmitry Korzhnev's paper at DOI: 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 1H SQ data will be optimised. The values found by cpmg_fit using just this data are:

• r2 = {'500': 6.691697587650816, '600': 6.998915158708793, '800': 5.519267837559072},
• pA = 0.946949480545876,
• dwH = -0.265279672133308,
• kex = 406.548178869750700,
• chi2 = 50.400680290545026.

test_korzhnev_2005_all_data(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 DOI: 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.

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.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0509100103. This is CPMG data with a fixed relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride).

test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72_full(self)

Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0509100103. This is CPMG data with a fixed relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride).

test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_tsmfk01(self)

Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0509100103. This is CPMG data with a fixed relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride).

Figure 3 shows the ln( k_a [s^-1]) for different concentrations of GuHCl. The precise values are:

• [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
• 0.483 0.89623903 2.4503699912708878
• 0.545 1.1694838
• 0.545 1.1761503
• 0.622 1.294
• 0.669 1.5176493
• 0.722 1.6238791
• 0.813 1.9395758
• 1.011 2.3558415 10.547000429321157

test_kteilum_fmpoulsen_makke_cpmg_data_101m_guhcl_to_tsmfk01(self)

Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0509100103. This is CPMG data with a fixed relaxation time period. Experiment in 1.01 M GuHCl (guanidine hydrochloride).

The comparison is to Figure 2, which is for dataset with 1 M GuHCl. The reported results are expected to be in rad.s^-1. Conversion into relax stored values is preferably.

Representative 15N CPMG relaxation dispersion curve measured on the cross peaks from residue L61 in folded ACBP at pH 5.3, 1 M GuHCl, and 40C:

1. The dotted line represents a residue-specific fit of all parameters in Eq. 1:
   • k_AB = 11.3 +/- 0.7 s^-1,
   • dw = (2.45 +/- 0.09) * 10^3 s^-1,
   • R2 = 8.0 +/- 0.5 s^-1.
2. The solid line represents a global fit of k_AB to all protein residues and a residue-specific fit of dw and R2.:
   • k_AB = 10.55 +/- 0.08 s^-1,
   • dw = (2.44 +/- 0.08) * 10^3 s^-1,
   • R2 = 8.4 +/- 0.3 s^-1.

Conversion of paper results to relax results is performed by:

• dw(ppm) = dw(rad.s^-1) * 10^6 * 1/(2*pi) * (gyro1H/(gyro15N*spectrometer_freq)) = 2.45E3 * 1E6 / (2 * math.pi) * (26.7522212E7/(-2.7126E7 * 599.8908622E6)) = -6.41 ppm.

Figure 3 shows the ln( k_a [s^-1]) for different concentrations of GuHCl. The precise values are:

• [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
• 0.483 0.89623903 2.4503699912708878
• 0.545 1.1694838
• 0.545 1.1761503
• 0.622 1.294
• 0.669 1.5176493
• 0.722 1.6238791
• 0.813 1.9395758
• 1.011 2.3558415 10.547000429321157

test_r1rho_kjaergaard(self)

Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.

This uses the data from Kjaergaard's paper at DOI: 10.1021/bi4001062.

test_r20_from_min_r2eff_cpmg(self)

Test speeding up grid search. Support requst sr #3151 https://web.archive.org/web/https://gna.org/support/index.php?3151.

User function to set the R20 parameters in the default grid search using the minimum R2eff value.

Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius.

test_sod1wt_t25_bug_21954_order_error_analysis(self)

Error analysis of SOD1-WT CPMG. From paper at http://dx.doi.org/10.1073/pnas.0907387106.

Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius.

bug #21954 https://web.archive.org/web/https://gna.org/bugs/index.php?21954: Order of spectrum.error_analysis is important.

test_sod1wt_t25_to_cr72(self)

Optimisation of SOD1-WT CPMG. From paper at http://dx.doi.org/10.1073/pnas.0907387106.

Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius.

test_sod1wt_t25_to_sherekhan_input(self)

Conversion of SOD1-WT CPMG R2eff values into input files for sherekhan.

Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model.

This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius.

test_sprangers_data_to_mmq_cr72(self, model=None)

Test the 'MMQ CR72' 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 MMQ CPMG data with a fixed relaxation time period.

test_sprangers_data_to_ns_mmq_2site(self, model=None)

Test the 'NS MMQ 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.

test_value_write_calc_rotating_frame_params_int(self)

System test of the value.write function to write intensities for an R1rho setup. This system test is to make sure, that modifying the API for special parameters theta and w_eff does not alter the functionality value.write.

This uses the data of the saved state attached to bug #21344.

test_value_write_calc_rotating_frame_params_theta(self)

System test of the value.write function to write return values of theta from calc_rotating_frame_params() function for an R1rho setup.

This uses the data of the saved state attached to bug #21344.

test_value_write_calc_rotating_frame_params_w_eff(self)

System test of the value.write function to write return values of w_eff from calc_rotating_frame_params() function for an R1rho setup.

This uses the data of the saved state attached to bug #21344.

test_value_write_calc_rotating_frame_params_auto_analysis(self)

System test of the auto_analysis value.write function to write theta and w_eff values for an R1rho setup.

This uses the data of the saved state attached to bug #21344.