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Package test_suite :: Package system_tests :: Module n_state_model :: Class N_state_model
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Class N_state_model

source code

Class for testing various aspects specific to the N-state model.

Nested Classes [hide private]

Inherited from unittest.case.TestCase: failureException

Instance Methods [hide private]
 
__init__(self, methodName='runTest')
Skip some tests if scipy is not installed.		 source code
 
check_vectors(self)
Auxiliary method for checking the correct loading of bond vectors.		 source code
 
test_5_state_xz(self)
A 5-state model in the xz-plane (no pivotting of alpha).		 source code
 
test_A_to_chi(self)
Test the conversion of the alignment tensor to the chi tensor.		 source code
 
test_absolute_T(self)
Test the fitting of signless T values (J+D).		 source code
 
test_absolute_rdc(self)
Test the fitting of signless RDCs.		 source code
 
test_absolute_rdc_menthol(self)
Test the fitting of signless RDCs for menthol.		 source code
 
test_align_fit(self)
Test the use of RDCs and PCSs to find the alignment tensor.		 source code
 
test_align_fit_pcs(self)
Test the use of PCSs to find the alignment tensor.		 source code
 
test_align_fit_pcs_rand(self)
Test the use of randomised PCSs to find the alignment tensor.		 source code
 
test_align_fit_rand(self)
Test the use of randomised RDCs and PCSs to find the alignment tensor.		 source code
 
test_align_fit_rdc(self)
Test the use of RDCs to find the alignment tensor.		 source code
 
test_align_fit_rdc_rand(self)
Test the use of randomised RDCs to find the alignment tensor.		 source code
 
test_data_copying(self)
The copying of RDC and PCS data from one pipe to another.		 source code
 
test_frame_order_align_fit(self)
Test the use of alignment tensors, RDCs and PCSs from a frame order data pipe for the N-state model.		 source code
 
test_lactose_n_state_fixed(self)
The 4-state model analysis of lactose using RDCs and PCSs.		 source code
 
test_lactose_n_state_population(self)
The 4-state model analysis of lactose using RDCs and PCSs.		 source code
 
test_mc_sim_failure(self)
Test the setup of the Monte Carlo simulations		 source code
 
test_metal_pos_opt(self)
Test a certain algorithm for the optimisation of the lanthanide position using RDCs and PCSs (with missing data).		 source code
 
test_missing_data(self)
Test the use of RDCs and PCSs to find the alignment tensor with missing data.		 source code
 
test_monte_carlo_sims(self)
Test the Monte Carlo simulation data of fitting RDCs and PCSs.		 source code
 
test_paramag_align_fit(self)
Test the use of RDCs and PCSs to find the alignment tensor.		 source code
 
test_paramag_centre_fit(self)
Test the use of RDCs and PCSs to find the alignment tensor.		 source code
 
test_pcs_back_calc(self)
Test the back-calculation of PCSs for ubiquitin.		 source code
 
test_pcs_fit_true_pos(self)
Test the fit of DNA PCSs at the true Ln3+ position.		 source code
 
test_pcs_fit_zero_pos(self)
Test the fit of DNA PCSs at a Ln3+ position of [0, 0, 0].		 source code
 
test_pcs_to_rdc(self)
Test the back-calculation of RDCs from a PCS derived tensor.		 source code
 
test_populations(self)
Test the 'population' N-state model optimisation using RDCs and PCSs (with missing data).		 source code
 
test_pyrotartaric_anhydride_absT(self)
Pyrotarctic anhydride alignment tensor optimisation using long range (1J, 2J & 3J) absolute T (J+D) data.		 source code
 
test_pyrotartaric_anhydride_mix(self)
Pyrotarctic anhydride alignment tensor optimisation using short range RDC and long range (1J, 2J & 3J) absolute T (J+D) data.		 source code
 
test_pyrotartaric_anhydride_rdcs(self)
Pyrotarctic anhydride alignment tensor optimisation using long range (1J, 2J & 3J) RDC data.		 source code
 
test_rdc_tensor(self)
Test the calculation of an alignment tensor from RDC data.		 source code
 
test_stereochem_analysis(self)
The full relative stereochemistry analysis.		 source code
 
test_vector_loading1(self)
Test the loading of inter-atomic vectors in the 'population' N-state model.		 source code
 
test_vector_loading2(self)
Test the loading of inter-atomic vectors in the 'population' N-state model.		 source code
 
test_vector_loading3(self)
Test the loading of inter-atomic vectors in the 'population' N-state model.		 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, setUp, 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]

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

source code 

Skip some tests if scipy is not installed.

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

test_5_state_xz(self)

source code 

A 5-state model in the xz-plane (no pivotting of alpha).

The 5 states correspond to the Euler angles (z-y-z notation):

  • State 1: {0, pi/4, 0}
  • State 2: {0, pi/8, 0}
  • State 3: {0, 0, 0}
  • State 4: {0, -pi/8, 0}
  • State 5: {0, -pi/4, 0}

test_mc_sim_failure(self)

source code 

Test the setup of the Monte Carlo simulations

This failed when this test was added, and is probably due to missing data.


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