Class Structure

Class for testing the structural objects.

Nested Classes

Inherited from unittest.case.TestCase: failureException

Instance Methods

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

strip_remarks(self, lines)
Strip out all PDB remark lines.

test_add_secondary_structure(self)
Check the operation of the structure.add_helix and structure.add_sheet user functions.

test_align(self)
Test the structure.superimpose user function.

test_align_CaM_BLOSUM62(self)
Test the alignment of CaM molecules from different species using the BLOSUM62 substitution matrix.

test_align_molecules(self)
Test the structure.superimpose user function for aligning different molecules in one pipe.

test_align_molecules2(self)
Test of the structure.superimpose user function, fitting to the mean structure.

test_align_molecules_end_truncation(self)
Test of the structure.superimpose user function, fitting to the mean structure.

test_alt_loc_missing(self)
Test that a RelaxError occurs when the alternate location indicator is present but not specified.

test_atomic_fluctuations(self)
Check the operation of the structure.atomic_fluctuations user function.

test_atomic_fluctuations_angle(self)
Check the angular fluctuations calculated by the structure.atomic_fluctuations user function.

test_atomic_fluctuations_gnuplot(self)
Check the operation of the structure.atomic_fluctuations user function for creating a gnuplot script.

test_atomic_fluctuations_no_match(self)
Check the operation of the structure.atomic_fluctuations user function when no data matches the atom ID.

test_atomic_fluctuations_parallax(self)
Check the parallax shift fluctuations calculated by the structure.atomic_fluctuations user function.

test_bug_12_hash_in_mol_name_via_arg(self)
Catch bug #12, the failure to detect '#' in the molecule name.

test_bug_12_hash_in_mol_name_via_file(self)
Catch bug #12, the failure to detect '#' in the molecule name.

test_bug_20470_alternate_location_indicator(self)
Catch bug #20470, the alternate location indicator problem.

test_bug_21187_corrupted_pdb(self)
Catch bug #21187, the corrupted PDB with all proton atoms numbers set to zero.

test_bug_21522_master_record_atom_count(self)
Catch bug #21522, the structure.write_pdb user function creating an incorrect MASTER record.

test_bug_21814_pdb_no_80_space_padding(self)
Catch bug #21814, the PDB reading failure when not padded to 80 spaces.

test_bug_22041_atom_numbering(self)
Catch bug #22041, the atom serial number not being sequential from 1 onwards.

test_bug_22069_structure_delete_helix_attribute(self)
Catch bug #22069, the failure of the structure.delete user function with helix attribute errors.

test_bug_22070_structure_superimpose_after_deletion(self)
Catch bug #22070, the failure of the structure.superimpose user function after deleting atoms with structure.delete.

test_bug_22860_CoM_after_deletion(self)
Catch bug #22860, the failure of the structure.com user function after calling structure.delete.

test_bug_22861_PDB_writing_chainID_fail(self)
Catch bug #22861, the chain IDs in the structure.write_pdb user function PDB files are incorrect after calling structure.delete.

test_bug_23293_missing_hetatm(self)
Catch bug #23293, the PDB HETATM loading error whereby the last HETATM record is sometimes not read from the PDB file.

test_bug_23294_multi_mol_automerge(self)
Catch bug #23294, the automatic merging of PDB molecules results in an IndexError.

test_bug_23295_ss_metadata_merge(self)
Catch bug #23295, the PDB secondary structure HELIX and SHEET records not updated when merging molecules.

test_bug_sr_2998_broken_conect_records(self)
Test the bug reported as the support request #2998, the broken CONECT records.

test_collapse_ensemble(self)
Test the collapse_ensemble() method of the internal structural object.

test_create_diff_tensor_pdb(self)
Test the deletion of non-existent structural data.

test_create_diff_tensor_pdb2(self)
Test the creation of the diffusion tensor PDB representation, after deleting structural data.

test_create_diff_tensor_pdb_ellipsoid(self)
Check that the ellipsoid diffusion tensor optimisation functions correctly.

test_create_diff_tensor_pdb_oblate(self)
Check the 3D coordinates of the PDB representation of the optimised oblate diffusion tensor.

test_create_diff_tensor_pdb_prolate(self)
Check the 3D coordinates of the PDB representation of the optimised prolate diffusion tensor.

test_create_diff_tensor_pdb_sphere(self)
Check that the sphere diffusion tensor optimisation functions correctly.

test_delete_atom(self)
Test the deletion of a single atom using the structure.delete user function

test_delete_empty(self)
Test the deletion of non-existent structural data.

test_delete_model(self)
Test the deletion of a single structural model.

test_delete_multi_pipe(self)
Test the deletion of structural data in only one pipe.

test_displacement(self)
Test of the structure.displacement user function.

test_displacement_molecules(self)
Test of the structure.displacement user function for different molecules in one pipe.

test_find_pivot(self)
Test the structure.find_pivot user function.

test_find_pivot_molecules(self)
Test the structure.find_pivot user function.

test_get_model(self)
Test the get_model() method of the internal structural object.

test_load_internal_results(self)
Load the PDB file using the information in a results file (using the internal structural object).

test_load_internal_results2(self)
Load the PDB file using the information in a results file (using the internal structural object).

test_load_spins_mol_cat(self)
Test the loading of spins from different molecules into one molecule container.

test_load_spins_multi_mol(self)
Test the structure.load_spins user function for loading the same spins from multiple molecules.

test_mean(self)
Test the structure.mean user function.

test_mean_models(self)
Test the structure.mean user function for different models.

test_mean_molecules(self)
Test the structure.mean user function for different molecules in one pipe.

test_metadata_xml(self)
Test the storage and loading of metadata into an XML state file.

test_multi_model_and_multi_molecule(self)
Test the loading and writing of a multi-model and multi-molecule PDB file.

test_pca(self)
Test the principle component analysis of the structure.pca user function.

test_pca_observers(self)
Test the principle component analysis of the structure.pca user function while using observer molecules.

test_pdb_combined_secondary_structure(self)
Test the handling of secondary structure metadata when combining multiple PDB structures.

test_read_gaussian_strychnine(self)
Load the structure from the 'strychnine_opt_cdcl3_b3lyp_gaussian.log.bz2' compressed Gaussian log file.

test_read_merge(self)
Test the merging of two molecules into one.

test_read_merge_simultaneous(self)
Test the simultaneous merging of two molecules into one.

test_read_not_pdb(self)
Test the reading of a file by structure.read_pdb that is not a PDB.

test_read_pdb_1UBQ(self)
Test the reading of the complete 1UBQ PDB file.

test_read_pdb_complex_internal(self)
Test the packing of models and molecules using 'gromacs.pdb' and 'lactose_MCMM4_S1_*.pdb' (using the internal structural object PDB reader).

test_read_pdb_internal1(self)
Load the '1F35_N_H_molmol.pdb' PDB file (using the internal structural object PDB reader).

test_read_pdb_internal2(self)
Load the 'Ap4Aase_res1-12.pdb' PDB file (using the internal structural object PDB reader).

test_read_pdb_internal3(self)
Load the 'gromacs.pdb' PDB file (using the internal structural object PDB reader).

test_read_pdb_internal4(self)
Load the 'tylers_peptide_trunc.pdb' PDB file (using the internal structural object PDB reader).

test_read_pdb_internal5(self)
Load the 'lactose_MCMM4_S1_1.pdb' PDB file (using the internal structural object PDB reader).

test_read_pdb_internal6(self)
Load the 'lactose_MCMM4_S1_1.pdb' and 'lactose_MCMM4_S1_2.pdb' PDB files as 2 separate structures (using the internal structural object PDB reader).

test_read_pdb_internal7(self)
Load the 'lactose_MCMM4_S1_1.pdb' PDB file twice as 2 separate structures (using the internal structural object PDB reader).

test_read_pdb_model_2_mol_internal(self)
Load the 2 models of the 'gromacs.pdb' PDB file as separate molecules of the same model (using the internal structural object PDB reader).

test_read_pdb_mol_2_model_internal(self)
Load a few 'lactose_MCMM4_S1_*.pdb' PDB files as models (using the internal structural object PDB reader).

test_read_write_pdb_1UBQ(self)
Test the reading and writing of the 1UBQ PDB file.

test_read_xyz_internal1(self)
Load the 'Indol_test.xyz' XYZ file (using the internal structural object XYZ reader).

test_read_xyz_internal2(self)
Load the 'SSS-cluster4-new-test.xyz' XYZ file (using the internal structural object XYZ reader).

test_read_xyz_strychnine(self)
Load the 'strychnine.xyz' XYZ file (using the internal structural object XYZ reader).

test_rmsd(self)
Test the structure.rmsd user function.

test_rmsd_molecules(self)
Test the structure.rmsd user function for different molecules in one pipe.

test_rmsd_spins(self)
Test the structure.rmsd user function for per-atom RMSDs.

test_rmsd_ubi(self)
Test the structure.rmsd user function on the truncated ubiquitin ensemble.

test_sequence_alignment_central_star_nw70_blosum62(self)
Test of the structure.sequence_alignment user function using the 'Central Star', 'NW70', and 'BLOSUM62' options.

test_sequence_alignment_residue_number(self)
Test of the structure.sequence_alignment user function using the 'residue number' MSA algorithm.

test_superimpose_fit_to_first(self)
Test of the structure.superimpose user function, fitting to the first structure.

test_superimpose_fit_to_mean(self)
Test of the structure.superimpose user function, fitting to the mean structure.

test_superimpose_fit_to_mean2(self)
Second test of the structure.superimpose user function, fitting to the mean structure.

test_web_of_motion_12(self)
Check the operation of the structure.web_of_motion user function using structural models 1 and 2 (of 3).

test_web_of_motion_12_molecules(self)
Check the operation of the structure.web_of_motion user function using molecules 1 and 2 (of 3).

test_web_of_motion_13(self)
Check the operation of the structure.web_of_motion user function using structural models 1 and 3 (of 3).

test_web_of_motion_13_molecules(self)
Check the operation of the structure.web_of_motion user function using molecules 1 and 3 (of 3).

test_web_of_motion_all(self)
Check the operation of the structure.web_of_motion user function using all structural models.

test_web_of_motion_all_molecules(self)
Check the operation of the structure.web_of_motion user function using all molecules.

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

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

setUp(self)

Set up for all the functional tests.

Overrides: unittest.case.TestCase.setUp

strip_remarks(self, lines)

Strip out all PDB remark lines.

Parameters:

• lines (list of str) - The list of PDB lines.

test_atomic_fluctuations(self)

Check the operation of the structure.atomic_fluctuations user function.

This checks the interatomic distance fluctuations calculated by the structure.atomic_fluctuations user function.

test_atomic_fluctuations_angle(self)

Check the angular fluctuations calculated by the structure.atomic_fluctuations user function.

This checks the text file (with the format argument set to text) of interatomic angle fluctuations calculated by the structure.atomic_fluctuations user function.

test_atomic_fluctuations_gnuplot(self)

Check the operation of the structure.atomic_fluctuations user function for creating a gnuplot script.

This checks the format argument of the structure.atomic_fluctuations user function when set to 'gnuplot'.

test_atomic_fluctuations_no_match(self)

Check the operation of the structure.atomic_fluctuations user function when no data matches the atom ID.

This checks the interatomic distance fluctuations calculated by the structure.atomic_fluctuations user function.

test_atomic_fluctuations_parallax(self)

Check the parallax shift fluctuations calculated by the structure.atomic_fluctuations user function.

This checks the text file (with the format argument set to text) of interatomic parallax shift fluctuations calculated by the structure.atomic_fluctuations user function.

test_bug_12_hash_in_mol_name_via_arg(self)

Catch bug #12, the failure to detect '#' in the molecule name.

This is for the case where set_mol_name argument value contains the '#' character. The test checks both the structure.read_pdb and structure.read_xyz user functions.

test_bug_12_hash_in_mol_name_via_file(self)

Catch bug #12, the failure to detect '#' in the molecule name.

This is for the case where the PDB file itself contains the '#' character. The test checks both the structure.read_pdb and structure.read_xyz user functions.

test_bug_21522_master_record_atom_count(self)

Catch bug #21522, the structure.write_pdb user function creating an incorrect MASTER record.

This also triggers bug #21520, the failure of the structure.write_pdb user function when creating the MASTER record due to too many ATOM and HETATM records being present.

test_displacement_molecules(self)

Test of the structure.displacement user function for different molecules in one pipe.

This checks the molecules argument of the structure.displacement user function.

test_find_pivot(self)

Test the structure.find_pivot user function.

This checks the default operation of the structure.find_pivot user function.

test_find_pivot_molecules(self)

Test the structure.find_pivot user function.

This checks the structure.find_pivot user function when the molecules argument is given.

test_mean_models(self)

Test the structure.mean user function for different models.

This checks the molecules argument of the structure.mean user function.

test_mean_molecules(self)

Test the structure.mean user function for different molecules in one pipe.

This checks the molecules argument of the structure.mean user function.

test_rmsd_molecules(self)

Test the structure.rmsd user function for different molecules in one pipe.

This checks the molecules argument of the structure.rmsd user function.