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Package test_suite :: Package system_tests :: Module model_free :: Class Mf
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Class Mf

source code

TestCase class for the functional tests of model-free analysis.

Nested Classes [hide private]

Inherited from unittest.case.TestCase: failureException

Instance Methods [hide private]
 
setUp(self)
Set up for all the functional tests.		 source code
 
check_read_results_1_3(self)
Common code for the test_read_results_1_3*() tests.		 source code
str
mesg_opt_debug(self, spin)
Method for returning a string to help debug the minimisation.		 source code
 
monte_carlo(self)
Run Monte Carlo simulations for the optimised model-free model.		 source code
 
object_comparison(self, obj1=None, obj2=None, skip=None)
Check if the contents of 2 objects are the same.		 source code
 
test_bug_14872_unicode_selection(self)
Test catching bug #14872, the unicode string selection failure as submitted by Olivier Serve.		 source code
 
test_bug_14941_local_tm_global_selection(self)
Test catching bug #14941, the local tm global model selection problem as submitted by Mikaela Stewart (mikaela dot stewart att gmail dot com).		 source code
 
test_bug_15050(self)
Test catching bug #15050, 'PipeContainer' object has no attribute 'diff_tensor' error as submitted by Tiago Pais.		 source code
 
test_bugs_12582_12591_12607(self)
Test catching bugs #12582, #12591 and #12607 as submitted by Chris Brosey.		 source code
 
test_bug_18790(self)
Test catching bug #18790, the negative relaxation data RelaxError reported by Vitaly Vostrikov.		 source code
 
test_bug_20213_asn_sidechain(self)
Bug #20213 catch, the model selection failure due to the presence of Asp and Gln sidechain N spins.		 source code
 
test_bug_20464_missing_ri_data(self)
Bug #20464 catch, the failure due to missing relaxation data.		 source code
 
test_bug_20563_missing_ri_error(self)
Bug #20563 catch, the failure due to missing relaxation data errors.		 source code
 
test_bug_20531_molmol_macro_write_relaxfault(self)
Bug #20531 catch, the RelaxFault when creating the Molmol macros.		 source code
 
test_bug_20531_molmol_macro_write_relaxfault2(self)
Bug #20531 catch, the RelaxFault when creating the Molmol macros.		 source code
 
test_bug_20613_auto_mf_diff_tensor_pdb(self)
Bug #20613 catch, the failure of the auto-analysis due to diffusion tensor PDB creation for the local tm global model.		 source code
 
test_bug_20683_bdc_inf_values(self)
Catch bug #20683, the model-free analysis failure due to infinite values in the Bruker Dynamics Centre files.		 source code
 
test_bug_21079_local_tm_global_selection(self)
Test catching bug #21079, the local tm global model selection.		 source code
 
test_create_m4(self)
Creating model m4 with parameters {S2, te, Rex} using model_free.create_model().		 source code
 
test_dauvergne_protocol(self)
Check the execution of auto_analyses.dauvergne_protocol.		 source code
 
test_generate_ri(self)
Back-calculate relaxation data.		 source code
 
test_latex_table(self)
Test the creation of a LaTeX table of model-free results, mimicking the latex_mf_table.py sample script.		 source code
 
test_local_tm_10_S2_0_8_te_40(self)
Test the optimisation of the test set {tm=10, S2=0.8, te=40}.		 source code
 
test_local_tm_10_S2_0_8_te_40_test2(self)
Test the optimisation of the test set {tm=10, S2=0.8, te=40}.		 source code
 
test_local_tm_10_S2_0_8_te_40_test3(self)
Test the optimisation of the test set {tm=10, S2=0.8, te=40}.		 source code
 
test_m0_grid(self)
Test the optimisation of the m0 model-free model against the tm0 parameter grid.		 source code
 
test_m0_grid_vs_m1(self)
Test the optimisation of the m1 model-free model against the tm0 parameter grid.		 source code
 
test_m0_grid_vs_m2(self)
Test the optimisation of the m2 model-free model against the tm0 parameter grid.		 source code
 
test_m0_grid_vs_m3(self)
Test the optimisation of the m3 model-free model against the tm0 parameter grid.		 source code
 
test_m0_grid_vs_m4(self)
Test the optimisation of the m4 model-free model against the tm0 parameter grid.		 source code
 
test_m1_grid(self)
Test the optimisation of the m1 model-free model against the tm1 parameter grid.		 source code
 
test_m2_grid(self)
Test the optimisation of the m2 model-free model against the tm2 parameter grid.		 source code
 
test_m2_grid_vs_m4(self)
Test the optimisation of the m4 model-free model against the tm2 parameter grid.		 source code
 
test_m3_grid(self)
Test the optimisation of the m3 model-free model against the tm3 parameter grid.		 source code
 
test_m4_grid(self)
Test the optimisation of the m4 model-free model against the tm4 parameter grid.		 source code
 
test_m5_grid(self)
Test the optimisation of the m5 model-free model against the tm5 parameter grid.		 source code
 
test_m6_grid(self)
Test the optimisation of the m6 model-free model against the tm6 parameter grid.		 source code
 
test_m7_grid(self)
Test the optimisation of the m7 model-free model against the tm7 parameter grid.		 source code
 
test_m8_grid(self)
Test the optimisation of the m8 model-free model against the tm8 parameter grid.		 source code
 
test_m9_grid(self)
Test the optimisation of the m9 model-free model against the tm9 parameter grid.		 source code
 
test_omp_analysis(self)
Try a very minimal model-free analysis on the OMP relaxation data.		 source code
 
test_opendx_s2_te_rex(self)
Mapping the {S2, te, Rex} chi2 space through the OpenDX user function dx.map().		 source code
 
test_opendx_theta_phi_da(self)
Mapping the {theta, phi, Da} chi2 space through the OpenDX user function dx.map().		 source code
 
test_opendx_tm_s2_te(self)
Mapping the {local_tm, S2, te} chi2 space through the OpenDX user function dx.map().		 source code
 
test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149(self)
Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, Rex=0.149}		 source code
 
test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149(self)
Constrained BFGS opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149}		 source code
 
test_opt_constr_cd_back_S2_0_970_te_2048_Rex_0_149(self)
Constrained coordinate descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149}		 source code
 
test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149(self)
Constrained coordinate descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149}		 source code
 
test_opt_constr_newton_gmw_back_S2_0_970_te_2048_Rex_0_149(self)
Constrained Newton opt, GMW Hessian mod, backtracking line search {S2=0.970, te=2048, Rex=0.149}		 source code
 
test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149(self)
Constrained Newton opt, GMW Hessian mod, More and Thuente line search {S2=0.970, te=2048, Rex=0.149}		 source code
 
test_opt_constr_sd_back_S2_0_970_te_2048_Rex_0_149(self)
Constrained steepest descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149}		 source code
 
test_opt_constr_sd_mt_S2_0_970_te_2048_Rex_0_149(self)
Constrained steepest descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149}		 source code
 
test_opt_grid_search_S2_0_970_te_2048_Rex_0_149(self)
Constrained grid search {S2=0.970, te=2048, Rex=0.149}.		 source code
 
test_read_relax_data(self)
Reading of relaxation data using the user function relax_data.read().		 source code
 
test_read_results_1_2(self)
Read a relax 1.2 model-free results file using the user function results.read().		 source code
 
test_read_results_1_2_pse4(self)
Read the truncated relax 1.2 model-free results file for PSE-4.		 source code
 
test_read_results_1_2_tem1(self)
Read the truncated relax 1.2 model-free results file for TEM-1.		 source code
 
test_read_results_1_3_v1(self)
Read a 1.3 model-free results file (relax XML version 1).		 source code
 
test_read_results_1_3_pre_py273_v1(self)
Read a 1.3 model-free results file (pre-Python 2.7.3, relax XML version 1).		 source code
 
test_read_results_1_3_v2(self)
Read a 1.3 model-free results file (relax XML version 2).		 source code
 
test_read_results_1_3_v2_broken(self)
Read a 1.3 model-free results file (relax XML version 2) with corrupted floats.		 source code
 
test_read_results_1_3_pre_py273_v2(self)
Read a 1.3 model-free results file (pre-Python 2.7.3, relax XML version 2).		 source code
 
test_select_m4(self)
Selecting model m4 with parameters {S2, te, Rex} using model_free.select_model().		 source code
 
test_set_csa(self)
Setting the CSA value through the user function value.set().		 source code
 
test_tm0_grid(self)
Test the optimisation of the tm0 model-free parameter grid.		 source code
 
test_tm1_grid(self)
Test the optimisation of the tm1 model-free parameter grid.		 source code
 
test_tm2_grid(self)
Test the optimisation of the tm2 model-free parameter grid.		 source code
 
test_tm3_grid(self)
Test the optimisation of the tm3 model-free parameter grid.		 source code
 
test_tm4_grid(self)
Test the optimisation of the tm4 model-free parameter grid.		 source code
 
test_tm5_grid(self)
Test the optimisation of the tm5 model-free parameter grid.		 source code
 
test_tm6_grid(self)
Test the optimisation of the tm6 model-free parameter grid.		 source code
 
test_tm7_grid(self)
Test the optimisation of the tm7 model-free parameter grid.		 source code
 
test_tm8_grid(self)
Test the optimisation of the tm8 model-free parameter grid.		 source code
 
test_tm9_grid(self)
Test the optimisation of the tm9 model-free parameter grid.		 source code
 
test_tylers_peptide(self)
Try a component of model-free analysis on Tyler Reddy's peptide data (truncated).		 source code
 
test_write_results(self)
Writing of model-free results using the user function results.write().		 source code
 
value_test(self, spin, select=True, local_tm=None, s2=None, s2f=None, s2s=None, te=None, tf=None, ts=None, rex=None, chi2=None, iter=None, f_count=None, g_count=None, h_count=None, warning=None)
Test the optimisation values.		 source code

Inherited from base_classes.SystemTestCase: __init__, 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 [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

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

setUp(self)

source code 

Set up for all the functional tests.

Overrides: unittest.case.TestCase.setUp

mesg_opt_debug(self, spin)

source code 

Method for returning a string to help debug the minimisation.

Parameters:
  • spin (SpinContainer instance) - The SpinContainer of the optimised spin.
Returns: str
The debugging string.

test_bug_20531_molmol_macro_write_relaxfault2(self)

source code 

Bug #20531 catch, the RelaxFault when creating the Molmol macros.

This was the first attempt at catching the bug, but it failed. However the code paths tested here are not tested in any other tests, so this system test will remain.

test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, Rex=0.149}

The optimisation options are:

  • BFGS optimisation.
  • Backtracking line search.
  • Constrained.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

Relevant links for this test are:

test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained BFGS opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149}

The optimisation options are:

  • BFGS optimisation.
  • More and Thuente line search.
  • Constrained.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

Relevant links for this test are:

test_opt_constr_cd_back_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained coordinate descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149}

The optimisation options are:

  • Coordinate descent optimisation.
  • Backtracking line search.
  • Constrained.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained coordinate descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149}

The optimisation options are:

  • Coordinate descent optimisation.
  • More and Thuente line search.
  • Constrained.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

Relevant links for this test are:

test_opt_constr_newton_gmw_back_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained Newton opt, GMW Hessian mod, backtracking line search {S2=0.970, te=2048, Rex=0.149}

The optimisation options are:

  • Newton optimisation.
  • GMW Hessian modification.
  • Backtracking line search.
  • Constrained.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

Relevant links for this test are:

test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained Newton opt, GMW Hessian mod, More and Thuente line search {S2=0.970, te=2048, Rex=0.149}

The optimisation options are:

  • Newton optimisation.
  • GMW Hessian modification.
  • More and Thuente line search.
  • Constrained.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

Relevant links for this test are:

test_opt_constr_sd_back_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained steepest descent opt, backtracking line search {S2=0.970, te=2048, Rex=0.149}

The optimisation options are:

  • Steepest descent optimisation.
  • Backtracking line search.
  • Constrained.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

test_opt_constr_sd_mt_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained steepest descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149}

The optimisation options are:

  • Steepest descent optimisation.
  • More and Thuente line search.
  • Constrained.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

test_opt_grid_search_S2_0_970_te_2048_Rex_0_149(self)

source code 

Constrained grid search {S2=0.970, te=2048, Rex=0.149}.

The optimisation options are:

  • Constrained grid search.

The true data set is:

  • S2 = 0.970
  • te = 2048 ps
  • Rex = 0.149 s^-1

test_read_results_1_3_v2_broken(self)

source code 

Read a 1.3 model-free results file (relax XML version 2) with corrupted floats.

The floats are deliberately mangled to test the IEEE-754 reading.


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