Class Mf

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

Nested Classes

Inherited from unittest.case.TestCase: failureException

Instance Methods

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

str mesg_opt_debug(self, spin)
Method for returning a string to help debug the minimisation.

monte_carlo(self)
Run Monte Carlo simulations for the optimised model-free model.

object_comparison(self, obj1=None, obj2=None, skip=None)
Check if the contents of 2 objects are the same.

test_bug_14872_unicode_selection(self)
Test catching bug #14872, the unicode string selection failure as submitted by Olivier Serve.

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).

test_bug_15050(self)
Test catching bug #15050, 'PipeContainer' object has no attribute 'diff_tensor' error as submitted by Tiago Pais (https://web.archive.org/web/https://gna.org/users/tpais).

test_bugs_12582_12591_12607(self)
Test catching bugs #12582, #12591 and #12607 as submitted by Chris Brosey.

test_bug_18790(self)
Test catching bug #18790, the negative relaxation data RelaxError reported by Vitaly Vostrikov.

test_create_m4(self)
Creating model m4 with parameters {S2, te, Rex} using model_free.create_model().

test_dauvergne_protocol(self)
Check the execution of auto_analyses.dauvergne_protocol.

test_generate_ri(self)
Back-calculate relaxation data.

test_latex_table(self)
Test the creation of a LaTeX table of model-free results, mimicking the latex_mf_table.py sample script.

test_local_tm_10_S2_0_8_te_40(self)
Test the optimisation of the test set {tm=10, S2=0.8, te=40}.

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}.

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}.

test_m0_grid(self)
Test the optimisation of the m0 model-free model against the tm0 parameter grid.

test_m0_grid_vs_m1(self)
Test the optimisation of the m1 model-free model against the tm0 parameter grid.

test_m0_grid_vs_m2(self)
Test the optimisation of the m2 model-free model against the tm0 parameter grid.

test_m0_grid_vs_m3(self)
Test the optimisation of the m3 model-free model against the tm0 parameter grid.

test_m0_grid_vs_m4(self)
Test the optimisation of the m4 model-free model against the tm0 parameter grid.

test_m1_grid(self)
Test the optimisation of the m1 model-free model against the tm1 parameter grid.

test_m2_grid(self)
Test the optimisation of the m2 model-free model against the tm2 parameter grid.

test_m2_grid_vs_m4(self)
Test the optimisation of the m4 model-free model against the tm2 parameter grid.

test_m3_grid(self)
Test the optimisation of the m3 model-free model against the tm3 parameter grid.

test_m4_grid(self)
Test the optimisation of the m4 model-free model against the tm4 parameter grid.

test_m5_grid(self)
Test the optimisation of the m5 model-free model against the tm5 parameter grid.

test_m6_grid(self)
Test the optimisation of the m6 model-free model against the tm6 parameter grid.

test_m7_grid(self)
Test the optimisation of the m7 model-free model against the tm7 parameter grid.

test_m8_grid(self)
Test the optimisation of the m8 model-free model against the tm8 parameter grid.

test_m9_grid(self)
Test the optimisation of the m9 model-free model against the tm9 parameter grid.

test_omp_analysis(self)
Try a very minimal model-free analysis on the OMP relaxation data.

test_opendx_s2_te_rex(self)
Mapping the {S2, te, Rex} chi2 space through the OpenDX user function dx.map().

test_opendx_theta_phi_da(self)
Mapping the {theta, phi, Da} chi2 space through the OpenDX user function dx.map().

test_opendx_tm_s2_te(self)
Mapping the {local_tm, S2, te} chi2 space through the OpenDX user function dx.map().

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}

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}

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}

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}

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}

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}

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}

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}

test_opt_grid_search_S2_0_970_te_2048_Rex_0_149(self)
Constrained grid search {S2=0.970, te=2048, Rex=0.149}.

test_read_relax_data(self)
Reading of relaxation data using the user function relax_data.read().

test_read_results_1_2(self)
Read a relax 1.2 model-free results file using the user function results.read().

test_read_results_1_2_pse4(self)
Read the truncated relax 1.2 model-free results file for PSE-4.

test_read_results_1_2_tem1(self)
Read the truncated relax 1.2 model-free results file for TEM-1.

test_read_results_1_3(self)
Read a relax 1.3 model-free results file using the user function results.read().

test_select_m4(self)
Selecting model m4 with parameters {S2, te, Rex} using model_free.select_model().

test_set_bond_length(self)
Setting the bond length through the user function value.set().

test_set_csa(self)
Setting the CSA value through the user function value.set().

test_set_csa_bond_length(self)
Setting both the CSA value and bond length through the user function value.set().

test_tm0_grid(self)
Test the optimisation of the tm0 model-free parameter grid.

test_tm1_grid(self)
Test the optimisation of the tm1 model-free parameter grid.

test_tm2_grid(self)
Test the optimisation of the tm2 model-free parameter grid.

test_tm3_grid(self)
Test the optimisation of the tm3 model-free parameter grid.

test_tm4_grid(self)
Test the optimisation of the tm4 model-free parameter grid.

test_tm5_grid(self)
Test the optimisation of the tm5 model-free parameter grid.

test_tm6_grid(self)
Test the optimisation of the tm6 model-free parameter grid.

test_tm7_grid(self)
Test the optimisation of the tm7 model-free parameter grid.

test_tm8_grid(self)
Test the optimisation of the tm8 model-free parameter grid.

test_tm9_grid(self)
Test the optimisation of the tm9 model-free parameter grid.

test_tylers_peptide(self)
Try a component of model-free analysis on Tyler Reddy's peptide data (truncated).

test_write_results(self)
Writing of model-free results using the user function results.write().

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.

Inherited from base_classes.SystemTestCase: __init__, 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

Properties

Inherited from object: __class__

Method Details

setUp(self)

Set up for all the functional tests.

Overrides: unittest.case.TestCase.setUp

mesg_opt_debug(self, spin)

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_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}

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

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}

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

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}

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)

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

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}

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

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}

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

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}

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)

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)

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