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Package test_suite :: Package system_tests :: Module relax_disp :: Class Relax_disp
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type Relax_disp

source code

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

Nested Classes [hide private]

Inherited from unittest.case.TestCase: failureException

Instance Methods [hide private]
 
__init__(self, methodName='runTest')
Skip certain tests if the C modules are non-functional.		 source code
 
setUp(self)
Set up for all the functional tests.		 source code
 
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.		 source code
 
setup_r1rho_kjaergaard(self, cluster_ids=[], read_R1=True)
Set up the data for the test_r1rho_kjaergaard_*() system tests.		 source code
 
setup_hansen_cpmg_data(self, model=None)
Set up the data for the test_hansen_cpmg_data_*() system tests.		 source code
 
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.		 source code
 
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.		 source code
 
setup_sod1wt_t25(self, pipe_name, pipe_type, pipe_name_r2eff, select_spin_index)
Setup of data SOD1-WT CPMG.		 source code
 
setup_missing_r1_spins(self)
Function for setting up a few spins for the given pipe.		 source code
 
setup_paul_schanda_nov_2015(self, outdir=None)
This setup the truncated private data which was provided by Paul Schanda.		 source code
 
setup_tp02_data_to_ns_r1rho_2site(self, clustering=False)
Setup data for the test of relaxation dispersion 'NS R1rho 2-site' model fitting against the 'TP02' test data.		 source code
 
test_baldwin_synthetic(self)
Test synthetic data of Andrew J.		 source code
 
test_baldwin_synthetic_full(self)
Test synthetic data of Andrew J.		 source code
 
x_test_bmrb_sub_cpmg(self)
Task #7858: Make it possible to submit CPMG experiments for BMRB.		 source code
 
test_bug_21081_disp_cluster_fail(self)
Bug #21081 catch, the failure of a cluster analysis when spins are deselected.		 source code
 
test_bug_21460_disp_cluster_fail(self)
Bug #21460 catch, the failure due to a spectrometer frequency having no relaxation data.		 source code
 
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.		 source code
 
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 minimise.calculate().		 source code
 
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.		 source code
 
test_bug_21715_clustered_indexerror(self)
Catch bug #21715, the failure of a clustered auto-analysis due to an IndexError.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
test_bug_22477_grace_write_k_AB_mixed_analysis(self)
Catch bug #22146, the failure of issuing: grace.write(x_data_type='res_num', y_data_type=param) for a mixed CPMG analysis.		 source code
 
test_bug_23186_cluster_error_calc_dw(self)
Catch bug #23186: Error calculation of individual parameter "dw" from Monte-Carlo, is based on first spin.		 source code
 
test_bug_24601_r2eff_missing_data(self)
Catch bug #24601, the failure of optimisation of the 'R2eff' model with missing data.		 source code
 
test_bug_9999_slow_r1rho_r2eff_error_with_mc(self)
Catch bug #9999, The slow optimisation of R1rho R2eff error estimation with Monte Carlo simulations.		 source code
 
test_bug_atul_srivastava(self)
Test data from Atul Srivastava.		 source code
 
test_bug_negative_intensities_cpmg(self)
Test data, where peak intensities are negative in CPMG		 source code
 
test_bug_seriestab_format(self)
Test data, where the format of SeriesTab format is different.		 source code
 
test_check_missing_r1(self)
Test of the check_missing_r1() function.		 source code
 
test_cpmg_synthetic_b14_to_ns3d_cluster(self)
Test synthetic cpmg data.		 source code
 
test_cpmg_synthetic_b14_to_ns_star_cluster(self)
Test synthetic cpmg data.		 source code
 
test_cpmg_synthetic_ns3d_to_cr72(self)
Test synthetic cpmg data.		 source code
 
test_cpmg_synthetic_ns3d_to_b14(self)
Test synthetic cpmg data.		 source code
 
test_cpmg_synthetic_ns3d_to_cr72_noise_cluster(self)
Test synthetic cpmg data.		 source code
 
test_cpmg_synthetic_dx_map_points(self)
Test synthetic cpmg data, calling the dx.map function with one or two points.		 source code
 
test_curve_type_cpmg_fixed_time(self)
Test the curve type detection using the Dr.		 source code
 
test_curve_type_r1rho_exponential(self, model=None)
Test the curve type detection using the 'M61' exponential test data.		 source code
 
test_curve_type_r1rho_fixed_time(self, model=None)
Test the curve type detection using the 'TP02' fixed time test data.		 source code
 
test_dpl94_data_to_dpl94(self)
Test the relaxation dispersion 'DPL94' model curve fitting to fixed time synthetic data.		 source code
 
test_dx_map_clustered(self)
Test making dx_map for residues under clustered calculation.		 source code
 
test_dx_map_clustered_create_par_file(self)
Test making dx_map for residues under clustered calculation, and the creation of the parameter file.		 source code
 
test_estimate_r2eff_err(self)
Test the user function for estimating R2eff errors from exponential curve fitting.		 source code
 
test_estimate_r2eff_err_auto(self)
Test the user function for estimating R2eff errors from exponential curve fitting, via the auto_analyses menu.		 source code
 
test_estimate_r2eff_err_methods(self)
Test the user function for estimating R2eff and associated errors for exponential curve fitting with different methods.		 source code
 
test_exp_fit(self)
Test the relaxation dispersion 'exp_fit' model curve fitting.		 source code
 
test_finite_value(self)
Test return from C code, when parameters are wrong.		 source code
 
test_hansen_catia_input(self)
Conversion of Dr.		 source code
 
test_hansen_cpmg_data_auto_analysis(self)
Test of the dispersion auto-analysis using Dr.		 source code
 
test_hansen_cpmg_data_auto_analysis_numeric(self)
Test of the numeric model only dispersion auto-analysis using Dr.		 source code
 
test_hansen_cpmg_data_auto_analysis_r2eff(self)
Test of the dispersion auto-analysis using Dr.		 source code
 
test_hansen_cpmg_data_missing_auto_analysis(self)
Test of the dispersion auto-analysis using Dr.		 source code
 
test_hansen_cpmg_data_to_cr72(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_cr72_full(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_it99(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_lm63(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_lm63_3site(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_ns_cpmg_2site_3D_full(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_ns_cpmg_2site_expanded(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_ns_cpmg_2site_star(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmg_data_to_ns_cpmg_2site_star_full(self)
Optimisation of Dr.		 source code
 
test_hansen_cpmgfit_input(self)
Conversion of Dr.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
test_korzhnev_2005_all_data(self)
Optimisation of all the Korzhnev et al., 2005 CPMG data using the 'NS MMQ 2-site' model.		 source code
 
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.		 source code
 
test_kteilum_fmpoulsen_makke_check_graphs(self)
Check of all possible dispersion graphs from optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
test_lm63_3site_synthetic(self)
Test the 'LM63 3-site' dispersion model using the pure noise-free synthetic data.		 source code
 
test_m61_data_to_m61(self)
Test the relaxation dispersion 'M61' model curve fitting to fixed time synthetic data.		 source code
 
test_m61_exp_data_to_m61(self)
Test the relaxation dispersion 'M61' model curve fitting to the full exponential synthetic data.		 source code
 
test_m61b_data_to_m61b(self)
Test the relaxation dispersion 'M61 skew' model curve fitting to fixed time synthetic data.		 source code
 
test_model_nesting_and_param(self)
Test that all models which can nest, have all their parameters converted.		 source code
 
test_ns_mmq_3site(self)
Compare the 'NS MMQ 3-site' dispersion model to synthetic data from cpmg_fit.		 source code
 
test_ns_mmq_3site_linear(self)
Compare the 'NS MMQ 3-site linear' dispersion model to synthetic data from cpmg_fit.		 source code
 
test_ns_r1rho_3site(self)
Compare the 'NS R1rho 3-site' dispersion model to synthetic data from cpmg_fit.		 source code
 
test_ns_r1rho_3site_linear(self)
Compare the 'NS R1rho 3-site linear' dispersion model to synthetic data from cpmg_fit.		 source code
 
test_paul_schanda_nov_2015(self)
This test truncated private data which was provided by Paul Schanda.		 source code
 
test_repeat_cpmg(self)
Test the protocol for repeated dispersion analysis.		 source code
 
test_r1rho_kjaergaard_auto(self)
Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.		 source code
 
test_r1rho_kjaergaard_auto_check_graphs(self)
Check of plot_disp_curves() function, after optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'R2eff' model.		 source code
 
test_r1rho_kjaergaard_missing_r1(self)
Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.		 source code
 
test_r2eff_read(self)
Test the operation of the relax_disp.r2eff_read user function.		 source code
 
test_r2eff_read_spin(self)
Test the operation of the relax_disp.r2eff_read_spin user function.		 source code
 
test_r2eff_fit_fixed_time(self)
Test the relaxation dispersion 'R2eff' model for fixed time data in the auto-analysis.		 source code
 
test_read_r2eff(self)
Test the reading of a file containing r2eff values.		 source code
 
test_r20_from_min_r2eff_cpmg(self)
Test speeding up grid search.		 source code
 
test_show_apod_extract(self)
Test getting the spectrum noise for spectrum fourier transformed with NMRPipe, and tool showApod.		 source code
 
test_show_apod_rmsd(self)
Test getting the spectrum noise for spectrum fourier transformed with NMRPipe, and tool showApod.		 source code
 
test_show_apod_rmsd_dir_to_files(self)
Test searching for all NMRPipe spectrum files in dir, call showApod, and write to files.		 source code
 
test_show_apod_rmsd_to_file(self)
Test getting the spectrum noise for spectrum fourier transformed with NMRPipe, and tool showApod, and write to file.		 source code
 
test_sod1wt_t25_bug_21954_order_error_analysis(self)
Error analysis of SOD1-WT CPMG.		 source code
 
test_sod1wt_t25_to_cr72(self)
Optimisation of SOD1-WT CPMG.		 source code
 
test_sod1wt_t25_to_sherekhan_input(self)
Conversion of SOD1-WT CPMG R2eff values into input files for sherekhan.		 source code
 
test_sprangers_data_to_mmq_cr72(self, model=None)
Test the 'MMQ CR72' model fitting against Remco Sprangers' ClpP data.		 source code
 
test_sprangers_data_to_ns_mmq_2site(self, model=None)
Test the 'NS MMQ 2-site' model fitting against Remco Sprangers' ClpP data.		 source code
 
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.		 source code
 
test_tp02_data_to_ns_r1rho_2site_cluster(self, model=None)
Test the relaxation dispersion 'NS R1rho 2-site' model fitting against the 'TP02' test data, when performing clustering.		 source code
 
test_tp02_data_to_mp05(self)
Test the dispersion 'MP05' model fitting against the 'TP02' test data.		 source code
 
test_tp02_data_to_tap03(self)
Test the dispersion 'TAP03' model fitting against the 'TP02' test data.		 source code
 
test_task_7882_monte_carlo_std_residual(self)
Implementation of Task #7882 https://web.archive.org/web/https://gna.org/task/?7882: Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals		 source code
 
x_test_task_7882_kex_conf(self)
Test related to Task #7882 https://web.archive.org/web/https://gna.org/task/?7882: Try making a confidence interval of kex.		 source code
 
test_tp02_data_to_tp02(self)
Test the relaxation dispersion 'TP02' model curve fitting to fixed time synthetic data.		 source code
 
test_value_write_calc_rotating_frame_params_int(self)
System test of the value.write function to write intensities for an R1rho setup.		 source code
 
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.		 source code
 
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.		 source code
 
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.		 source code
 
verify_estimate_r2eff_err_compare_mc(self)
Test the user function for estimating R2eff errors from exponential curve fitting, and compare it with Monte-Carlo simulations.		 source code
 
verify_r1rho_kjaergaard_missing_r1(self, models=None, result_dir_name=None, r2eff_estimate=None)
Verification of test_r1rho_kjaergaard_missing_r1.		 source code

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

Class Methods [hide private]

Inherited from unittest.case.TestCase: setUpClass, tearDownClass

Class Variables [hide private]

Inherited from unittest.case.TestCase: longMessage, maxDiff

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

Method Details [hide private]

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

source code 

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

Parameters:
  • methodName (str) - The name of the test.
Overrides: unittest.case.TestCase.__init__

setUp(self)

source code 

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)

source code 

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)

source code 

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)

source code 

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=[])

source code 

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)

source code 

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)

source code 

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)

source code 

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.

x_test_bmrb_sub_cpmg(self)

source code 

Task #7858: Make it possible to submit CPMG experiments for BMRB. This uses CPMG data from:

  • Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Soendergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE. Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations. (2011), Proteins: Struct, Funct, Bioinf 79(3):685-702, DOI 10.1002/prot.22886

test_bug_atul_srivastava(self)

source code 

Test data from Atul Srivastava. This is a bug missing raising a Relax Error, since the setup points to a situation where the data shows it is exponential fitting, but only one time point is added per file.

This follows: Thread: This follows: Thread: This follows: Thread:

test_bug_negative_intensities_cpmg(self)

source code 

Test data, where peak intensities are negative in CPMG

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_cpmg_synthetic_b14_to_ns3d_cluster(self)

source code 

Test synthetic cpmg data. Created with B14, analysed with NS CPMG 2site 3D, for clustered analysis.

This is part of: Task #7807: Speed-up of dispersion models for Clustered analysis.

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

test_cpmg_synthetic_b14_to_ns_star_cluster(self)

source code 

Test synthetic cpmg data. Created with B14, analysed with NS CPMG 2site STAR, for clustered analysis.

This is part of: Task #7807: Speed-up of dispersion models for Clustered analysis.

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

test_cpmg_synthetic_ns3d_to_cr72(self)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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

test_dx_map_clustered(self)

source code 

Test making dx_map for residues under clustered calculation.

This uses CPMG data from:

  • Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Soendergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations. (2011), Proteins: Struct, Funct, Bioinf 79(3):685-702, DOI 10.1002/prot.22886

test_dx_map_clustered_create_par_file(self)

source code 

Test making dx_map for residues under clustered calculation, and the creation of the parameter file.

Task #7860 : When dx_map is issued, create a parameter file which maps parameters to chi2 value.

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_estimate_r2eff_err(self)

source code 

Test the user function for estimating R2eff errors from exponential curve fitting.

This follows Task 7822. task #7822: Implement user function to estimate R2eff and associated errors for exponential curve fitting.

This uses the data from Kjaergaard's paper at DOI: 10.1021/bi4001062. Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.

test_estimate_r2eff_err_auto(self)

source code 

Test the user function for estimating R2eff errors from exponential curve fitting, via the auto_analyses menu.

This follows Task 7822. task #7822: Implement user function to estimate R2eff and associated errors for exponential curve fitting.

This uses the data from Kjaergaard's paper at DOI: 10.1021/bi4001062. Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.

test_estimate_r2eff_err_methods(self)

source code 

Test the user function for estimating R2eff and associated errors for exponential curve fitting with different methods. This is compared with a run where erros are estimated by 2000 Monte Carlo simulations.

This follows Task 7822. task #7822: Implement user function to estimate R2eff and associated errors for exponential curve fitting.

This uses the data from Kjaergaard's paper at DOI: 10.1021/bi4001062. Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.

NOTE: The difference in the methods was due to a bug in relax! bug #22554. The distribution of intensity with errors in Monte-Carlo simulations are markedly more narrow than expected.

This dataset is old, and includes 2000 Monte-Carlo simulations, which is performed wrong.

test_finite_value(self)

source code 

Test return from C code, when parameters are wrong. This can happen, if minfx takes a wrong step.

test_hansen_catia_input(self)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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_lm63_3site(self)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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_korzhnev_2005_all_data_disp_speed_bug(self)

source code 

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_check_graphs(self)

source code 

Check of all possible dispersion graphs from 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_048m_guhcl_to_cr72(self)

source code 

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)

source code 

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)

source code 

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)

source code 

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_paul_schanda_nov_2015(self)

source code 

This test truncated private data which was provided by Paul Schanda. This systemtest uncovers some unfortunate problems when running an analysis and reading points by the R2eff method.

test_repeat_cpmg(self)

source code 

Test the protocol for repeated dispersion analysis. The class: relax_disp_repeat_cpmg.

task #7826. Write an python class for the repeated analysis of dispersion data.

test_r1rho_kjaergaard_auto(self)

source code 

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.

This uses the automatic analysis.

test_r1rho_kjaergaard_auto_check_graphs(self)

source code 

Check of plot_disp_curves() function, after optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'R2eff' model.

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

This uses the automatic analysis.

test_r1rho_kjaergaard_missing_r1(self)

source code 

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.

This uses the automatic analysis, with missing loading R1.

test_r20_from_min_r2eff_cpmg(self)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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)

source code 

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.

x_test_task_7882_kex_conf(self)

source code 

Test related to Task #7882 https://web.archive.org/web/https://gna.org/task/?7882: Try making a confidence interval of kex. According to the regression book of Graphpad: http://www.graphpad.com/faq/file/Prism4RegressionBook.pdf. Page 109-111.

test_value_write_calc_rotating_frame_params_int(self)

source code 

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)

source code 

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)

source code 

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)

source code 

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.

verify_estimate_r2eff_err_compare_mc(self)

source code 

Test the user function for estimating R2eff errors from exponential curve fitting, and compare it with Monte-Carlo simulations.

This follows Task 7822. task #7822: Implement user function to estimate R2eff and associated errors for exponential curve fitting.

This uses the data from Kjaergaard's paper at DOI: 10.1021/bi4001062. Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model.


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