Class Frame_order

TestCase class for the functional tests of the frame order theories.

Nested Classes

Inherited from unittest.case.TestCase: failureException

Instance Methods

__init__(self, methodName='runTest', skip_tests=True)
Skip the tests if scipy is not installed.

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

tearDown(self)
Clean up after the tests.

check_chi2(self, chi2=0.0, places=1)
Check the function evaluation.

flags(self, rdc=True, pcs=True, opt=False)
Set a number of flags for the scripts.

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

space_probe(self, ref_chi2=None, params=None, delta=0.0523598775598)
Probe the space around the supposed minimum.

test_cam_double_rotor(self)
Test the double rotor frame order model of CaM.

test_cam_double_rotor_pcs(self)
Test the double rotor frame order model of CaM (with only PCS data).

test_cam_double_rotor_rdc(self)
Test the double rotor frame order model of CaM (with only RDC data).

test_cam_free_rotor(self)
Test the free rotor frame order model of CaM.

test_cam_free_rotor_missing_data(self)
Test the free rotor frame order model of CaM.

test_cam_free_rotor_pcs(self)
Test the free rotor frame order model of CaM (with only PCS data).

test_cam_free_rotor_rdc(self)
Test the free rotor frame order model of CaM (with only RDC data).

test_cam_free_rotor2(self)
Test the second free rotor frame order model of CaM.

test_cam_free_rotor2_pcs(self)
Test the second free rotor frame order model of CaM (with only PCS data).

test_cam_free_rotor2_rdc(self)
Test the second free rotor frame order model of CaM (with only RDC data).

test_cam_iso_cone(self)
Test the isotropic cone, free rotor frame order model of CaM.

test_cam_iso_cone_pcs(self)
Test the isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_iso_cone_rdc(self)
Test the isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_iso_cone_free_rotor(self)
Test the isotropic cone, free rotor frame order model of CaM.

test_cam_iso_cone_free_rotor_pcs(self)
Test the isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_iso_cone_free_rotor_rdc(self)
Test the isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_iso_cone_free_rotor2(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_iso_cone_free_rotor2_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_iso_cone_free_rotor2_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_iso_cone_torsionless(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_iso_cone_torsionless_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_iso_cone_torsionless_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_pseudo_ellipse(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_pseudo_ellipse_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_pseudo_ellipse_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_pseudo_ellipse2(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_pseudo_ellipse2_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_pseudo_ellipse2_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_pseudo_ellipse_free_rotor(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_pseudo_ellipse_free_rotor_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_pseudo_ellipse_free_rotor_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_pseudo_ellipse_torsionless(self)
Test the second isotropic cone, free rotor frame order model of CaM.

test_cam_pseudo_ellipse_torsionless_pcs(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only PCS data).

test_cam_pseudo_ellipse_torsionless_rdc(self)
Test the second isotropic cone, free rotor frame order model of CaM (with only RDC data).

test_cam_rigid(self)
Test the rigid frame order model of CaM.

test_cam_rigid_pcs(self)
Test the rigid frame order model of CaM (with only PCS data).

test_cam_rigid_rdc(self)
Test the rigid frame order model of CaM (with only RDC data).

test_cam_rotor(self)
Test the rotor frame order model of CaM.

test_cam_rotor_pcs(self)
Test the rotor frame order model of CaM (with only PCS data).

test_cam_rotor_rdc(self)
Test the rotor frame order model of CaM (with only RDC data).

test_cam_rotor_2_state(self)
Test the 2-state rotor frame order model of CaM.

test_cam_rotor_2_state_pcs(self)
Test the 2-state rotor frame order model of CaM (with only PCS data).

test_cam_rotor_2_state_rdc(self)
Test the 2-state rotor frame order model of CaM (with only RDC data).

test_cam_rotor2(self)
Test the second rotor frame order model of CaM.

test_cam_rotor2_pcs(self)
Test the second rotor frame order model of CaM (with only PCS data).

test_cam_rotor2_rdc(self)
Test the second rotor frame order model of CaM (with only RDC data).

test_generate_rotor2_distribution(self)
Generate the rotor2 distribution of CaM.

fixme_test_model_free_rotor(self)
Test the free rotor frame order model.

fixme_test_model_free_rotor_eigenframe(self)
Test the free rotor frame order model in the eigenframe.

fixme_test_model_iso_cone(self)
Test the isotropic cone frame order model.

fixme_test_model_iso_cone_free_rotor(self)
Test the free rotor isotropic cone frame order model.

fixme_test_model_iso_cone_free_rotor_eigenframe(self)
Test the free rotor isotropic cone frame order model in the eigenframe.

fixme_test_model_pseudo_ellipse(self)
Test the pseudo-ellipse frame order model.

fixme_test_model_pseudo_ellipse_free_rotor(self)
Test the free rotor pseudo-elliptic cone frame order model.

fixme_test_model_pseudo_ellipse_torsionless(self)
Test the pseudo-ellipse frame order model.

fixme_test_model_rotor(self)
Test the rotor frame order model.

fixme_test_model_rotor_eigenframe(self)
Test the rotor frame order model in the eigenframe.

fixme_test_opendx_map(self)
Test the mapping of the Euler angle parameters for OpenDx viewing.

fixme_test_opt_rigid_no_rot(self)
Test the 'rigid' model for unrotated tensors with no motion.

fixme_test_opt_rigid_rand_rot(self)
Test the 'rigid' model for randomly rotated tensors with no motion.

fixme_test_parametric_restriction_iso_cone_to_iso_cone_free_rotor(self)
Parametric restriction of the isotropic cone to the free rotor isotropic cone frame order model.

fixme_test_parametric_restriction_pseudo_ellipse_to_iso_cone(self)
Parametric restriction of the pseudo-ellipse to the isotropic cone frame order model.

fixme_test_parametric_restriction_pseudo_ellipse_to_iso_cone_free_rotor(self)
Parametric restriction of the pseudo-ellipse to the free rotor isotropic cone frame order model.

fixme_test_parametric_restriction_pseudo_ellipse_free_rotor_to_iso_cone(self)
Parametric restriction of the pseudo-ellipse to the isotropic cone frame order model.

fixme_test_parametric_restriction_pseudo_ellipse_free_rotor_to_iso_cone_free_rotor(self)
Parametric restriction of the free rotor pseudo-ellipse to the free rotor isotropic cone frame order model.

fixme_test_pseudo_ellipse(self)
Test the pseudo-ellipse target function.

fixme_test_pseudo_ellipse_torsionless(self)
Test the torsionless pseudo-ellipse target function.

test_rigid_data_to_free_rotor_model(self)
Test the free rotor target function for the data from a rigid test molecule.

test_rigid_data_to_iso_cone_model(self)
Test the iso cone target function for the data from a rigid test molecule.

test_rigid_data_to_iso_cone_free_rotor_model(self)
Test the iso cone, free rotor target function for the data from a rigid test molecule.

test_rigid_data_to_iso_cone_torsionless_model(self)
Test the iso cone, torsionless target function for the data from a rigid test molecule.

test_rigid_data_to_rigid_model(self)
Test the rigid target function for the data from a rigid test molecule.

test_rigid_data_to_rotor_model(self)
Test the rotor target function for the data from a rigid test molecule.

test_rigid_data_to_pseudo_ellipse_model(self)
Test the pseudo-ellipse target function for the data from a rigid test molecule.

test_rigid_data_to_pseudo_ellipse_torsionless_model(self)
Test the pseudo-ellipse, torsionless target function for the data from a rigid test molecule.

Inherited from base_classes.SystemTestCase: script_exec

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', skip_tests=True)
(Constructor)

Skip the tests if scipy is not installed.

Parameters:

• methodName (str) - The name of the test.
• skip_tests (bool) - A flag which if True will cause a large number of redundant tests to be skipped.

Overrides: object.__init__

setUp(self)

Set up for all the functional tests.

Overrides: unittest.case.TestCase.setUp

tearDown(self)

Clean up after the tests.

Overrides: unittest.case.TestCase.tearDown

mesg_opt_debug(self)

Method for returning a string to help debug the minimisation.

Returns: str

The debugging string.