tests package

Submodules

tests.test_CompareTargetMolecule module

Test the task CompareTargetMolecule

class tests.test_CompareTargetMolecule.TestCompareTargetMolecule(methodName='runTest')

Bases: TestCase

smiles_seq_to_xl_or_csv(ftype, property_seq=None, name_seq=None, feature_arr=None)

Helper method to convert a SMILES sequence or arbitrary features to Excel or CSV files.

Parameters

  • ftype (str) – String label to denote the filetype. ‘csv’ or ‘excel’.

  • property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses. Defaults to None.

  • name_seq (list or np.ndarray, optional) – Optional sequence of molecular names. Defaults to None.

  • feature_arr (np.ndarray, optional) – Optional array of molecular descriptor values. Defaults to None.

Raises

ValueError – Invalid file type specified.

Returns

Path to created file.

Return type

str

classmethod tearDownClass()

Delete temporary file used in testing.

test_get_molecule_least_similar_to()

Test for get_molecule_least_similar_to functionality.

test_get_molecule_most_similar_to()

tests.test_Descriptor module

Tests for the Descriptor class

class tests.test_Descriptor.TestDescriptor(methodName='runTest')

Bases: TestCase

Tests for methods of the Descriptor class.

Parameters

unittest (unittest) – Python unittest module.

test_bad_descriptors_padelpy_descriptors()

Test ability to pass through invalid descriptors to padelpy.

test_ccbmlib_descriptors()

Test ability to passthrough descriptors to ccbmlib.

test_descriptor_arbitrary_list_init()

Test to verify creation of Descriptor object initialized by arbitrary list.

test_descriptor_arbitrary_numpy_init()

Test to verify creation of Descriptor object initialized by arbitrary numpy array.

test_descriptor_empty_init()

Test to verify empty Descriptor object can be created.

test_descriptor_make_fingerprint()

Test to verify creation of Descriptor object by creating molecular fingerprints from the molecule graph.

test_exptl_descriptors()

Test ability to use experimental descriptors.

test_fingerprint_folding()

Create arbitrary fingerprint vector to check fold method

test_minhash_fingerprint()

Test creation of minhash fingerprint

test_mordred_descriptors()

Test ability to passthrough descriptors to Mordred.

test_nonexistent_mordred_descriptors()

Test ability to pass through descriptors to Mordred.

test_padelpy_descriptors()

Test ability to passthrough descriptors to PadelPy.

test_topological_fprint_min_path_lesser_than_atoms()

tests.test_LoadingErrorException module

Test the LoadingError Exception

class tests.test_LoadingErrorException.TestLoadingERrorException(methodName='runTest')

Bases: TestCase

Tests for LoadingError custom exception.

test_invalid_pdb()

Invalid PDB files should raise a LoadingError.

test_invalid_smiles()

Invalid SMILES strings should raise a LoadingError.

test_missing_pdb()

Missing PDB files should raise a LoadingError.

test_missing_smiles()

Missing smiles strings should raise a LoadingError.

tests.test_MeasureSearch module

Test the MeasureSearch class.

class tests.test_MeasureSearch.TestMeasureSearch(methodName='runTest')

Bases: TestCase

smiles_seq_to_textfile(property_seq=None)

Helper method to convert a SMILES sequence to a text file.

Parameters

property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses.. Defaults to None.

Returns

Path to created file.

Return type

str

test_error_optim_algo()

Measure search should error with invalid optimization algorithm.

test_fixed_SimilarityMeasure()

MeasureSearch should search for ideal fingerprint when metric is already chosen.

test_fixed_fprint()

MeasureSearch should search for ideal metric when fingerprint is already chosen.

test_logfile_generation()

When configured to do so, MeasureSearch should create a log file.

test_max_optim_algo()

Measure search using the “maximum” optimization algorithm.

test_min_optim_algo()

Measure search using the “minimum” optimization algorithm.

test_msearch_completion()

MeasureSearch should complete running, though output cannot be directly tested.

test_msearch_init()

Basic initialization test for the MeasureSearch class.

test_msearch_init_error()

Erroneous confirgurations should raise a config error.

Check that this configuration option is able to execute.

Check that this configuration option is able to execute.

Check that this configuration option is able to execute.

test_smiles = ['CCCCCCC', 'CCCC', 'CCC', 'CO', 'CN', 'C1=CC=CC=C1', 'CC1=CC=CC=C1', 'C(=O)(N)N']
test_verbose_output()

Ensure execution does not raise an exception with verbose and show_top.

tests.test_Molecule module

Test the methods of the Molecule class

class tests.test_Molecule.TestMolecule(methodName='runTest')

Bases: TestCase

Tests for methods of Molecule class.

test_get_name()

Retrieve the name from the molecule.

test_get_property_value()

Retrieve the property value from the molecule

test_is_same()

Two identical molecules should be identifed as such.

test_match_fprint_error()

Trying to match fingerprint from molecule w/o graph should throw an error.

test_mol_mol_similarity_w_morgan_tanimoto()

Test that the tanimoto similarity of the morgan fingerprints of two Molecules are in (0, 1).

test_mol_smiles_loadingerror()

Error in mol_smiles should raise LoadingError

test_mol_src_pdb_loadingerror()

Error in mol_src should raise LoadingError

test_mol_src_txt_loadingerror()

Error in mol_src should raise LoadingError

test_molecule_created_w_attributes()

Test to create Molecule object with descriptor value (list) and a response scalar.

test_molecule_created_with_no_attributes()

Test for creation of empty Molecule object with no attributes.

test_molecule_draw()

Test to draw molecule stored in Molecule object.

test_molecule_graph_similar_to_itself_morgan_dice()

Test that the morgan fingerprint of a Molecule object is similar to itself using dice similarity.

test_molecule_graph_similar_to_itself_morgan_l0()

Test that the morgan fingerprint of a Molecule object is similar to itself using L0 norm similarity.

test_molecule_graph_similar_to_itself_morgan_tanimoto()

Test that the morgan fingerprint of a Molecule object is similar to itself using Tanimoto similarity.

test_set_molecule_from_file()

Test to create Molecule object by reading the contents of a file.

Case #1: text file Case #2: PDB file

test_set_molecule_from_smiles()

Test to create Molecule object by reading SMILES string.

tests.test_MoleculeSet module

Test the MoleculeSet class.

class tests.test_MoleculeSet.TestMoleculeSet(methodName='runTest')

Bases: TestCase

get_feature_set(dimensionality=10)
smarts_seq_to_smiles_file(property_seq=None)

Helper method to convert a SMARTS sequence to a .SMILES file.

Parameters

property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses. Defaults to None.

Returns

Path to created file.

Return type

str

smiles_seq_to_pdb_dir(property_seq=None)

Helper method to convert a SMILES sequence to a pdb files stored in a directory.

Parameters

property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses. Defaults to None.

Returns

Path to created directory.

Return type

str

smiles_seq_to_smi_file(property_seq=None)

Helper method to convert a SMILES sequence to a .smi file.

Parameters

property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses. Defaults to None.

Returns

Path to created file.

Return type

str

smiles_seq_to_smiles_file(property_seq=None)

Helper method to convert a SMILES sequence to a .SMILES file.

Parameters

property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses. Defaults to None.

Returns

Path to created file.

Return type

str

smiles_seq_to_textfile(property_seq=None)

Helper method to convert a SMILES sequence to a text file.

Parameters

property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses.. Defaults to None.

Returns

Path to created file.

Return type

str

smiles_seq_to_xl_or_csv(ftype, property_seq=None, name_seq=None, feature_arr=None)

Helper method to convert a SMILES sequence or arbitrary features to Excel or CSV files.

Parameters

  • ftype (str) – String label to denote the filetype. ‘csv’ or ‘excel’.

  • property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses. Defaults to None.

  • name_seq (list or np.ndarray, optional) – Optional sequence of molecular names. Defaults to None.

  • feature_arr (np.ndarray, optional) – Optional array of molecular descriptor values. Defaults to None.

Raises

ValueError – Invalid file type specified.

Returns

Path to created file.

Return type

str

test_clustering_fingerprints()

Test the clustering of molecules featurized by their fingerprints.

test_get_most_dissimilar_pairs()

Test that all combinations of fingerprint_type and similarity measure works with the MoleculeSet.get_most_dissimilar_pairs() method.

test_get_most_similar_pairs()

Test that all combinations of fingerprint_type and similarity measure works with the MoleculeSet.get_most_similar_pairs() method.

test_invalid_transform_error()

Using an invalid or unimplemented dimensionality reduction method should throw an error.

test_isomap_transform()

Test the unsupervised transformation of molecules in MoleculSet using Isomap.

test_mds_transform()

Test the unsupervised transformation of molecules in MoleculSet using MDS.

test_molecule_set_getters()

Retrieve names and properties of mols using MoleculeSet.

test_molecule_set_sim_getters()

Get the properties for most and least similar molecule pairs.

test_pca_transform()

Test the unsupervised transformation of molecules in MoleculSet using Principal Component Analysis.

test_set_molecule_database_fingerprint_from_csv()

Verify that a TypeError is raised if no similarity_measure is specified when instantiating a MoleculeSet object.

test_set_molecule_database_from_csv()

Test to create MoleculeSet object by reading molecule database and molecular responses from a CSV file.

test_set_molecule_database_from_excel()

Test to create MoleculeSet object by reading molecule database from an Excel file.

test_set_molecule_database_from_excel_without_smiles_name()
test_set_molecule_database_from_pdb_dir()

Test to create MoleculeSet object by reading molecule database from a directory of pdb files.

test_set_molecule_database_from_smarts_file()

Test to create MoleculeSet object by reading molecule database from a SMILES file containing SMARTS strings.

test_set_molecule_database_from_smi_file()

Test to create MoleculeSet object by reading molecule database from a smi file.

test_set_molecule_database_from_smiles_file()

Test to create MoleculeSet object by reading molecule database from a SMILES file.

test_set_molecule_database_from_textfile()

Test to create MoleculeSet object by reading molecule database from a textfile.

test_set_molecule_database_w_descriptor_property_from_csv()

Test to create MoleculeSet object by reading molecule database containing arbitrary molecular descriptors and molecular responses from a CSV file.

test_set_molecule_database_w_descriptor_property_from_excel()

Test to create MoleculeSet object by reading molecule database containing arbitrary molecular descriptor values from an Excel file.

test_set_molecule_database_w_fingerprint_similarity_from_csv()

Test all combinations of fingerprints and similarity measures with the MoleculeSet class.

test_set_molecule_database_w_property_from_csv()

Test to create MoleculeSet object by reading molecule database and molecular responses from a CSV file.

test_set_molecule_database_w_property_from_excel()

Test to create MoleculeSet object by reading molecule database and molecular responses from an Excel file.

test_set_molecule_database_w_property_from_textfile()

Test to create MoleculeSet object by reading molecule database and molecular responses from a textfile.

test_set_molecule_database_w_similarity_from_csv()

Verify that a NotInitializedError is raised if no fingerprint_type is specified when instantiating a MoleculeSet object.

test_smarts = ['[CH3:1][S:2][c:3]1[cH:4][cH:5][c:6]([B:7]([OH:8])[OH:9])[cH:10][cH:11]1', '[NH:1]1[CH2:2][CH2:3][O:4][CH2:5][CH2:6]1.[O:7]=[S:8]=[O:9]']
test_smiles = ['CCCCCCC', 'CCCC', 'CCC', 'CO', 'CN', 'C1=CC=CC=C1', 'CC1=CC=CC=C1', 'C(=O)(N)N']
test_spectral_embedding_transform()

Test the unsupervised transformation of molecules in MoleculSet using Isomap.

test_subsample_molecule_database_from_csv()

Test to randomly subsample a molecule database loaded from an CSV file.

test_subsample_molecule_database_from_excel()

Test to randomly subsample a molecule database loaded from an Excel file.

test_subsample_molecule_database_from_pdb_dir()

Test to randomly subsample a molecule database loaded from a directory of pdb files.

test_subsample_molecule_database_from_textfile()

Test to randomly subsample a molecule database loaded from a textfile.

test_tsne_transform()

Test the unsupervised transformation of molecules in MoleculSet using TSNE.

tests.test_SimilarityMeasure module

Test the SimilarityMEasure class

class tests.test_SimilarityMeasure.TestSimilarityMeasure(methodName='runTest')

Bases: TestCase

smiles_seq_to_xl_or_csv(ftype, property_seq=None, name_seq=None, feature_arr=None)

Helper method to convert a SMILES sequence or arbitrary features to Excel or CSV files.

Parameters

  • ftype (str) – String label to denote the filetype. ‘csv’ or ‘excel’.

  • property_seq (list or np.ndarray, optional) – Optional sequence of molecular responses. Defaults to None.

  • name_seq (list or np.ndarray, optional) – Optional sequence of molecular names. Defaults to None.

  • feature_arr (np.ndarray, optional) – Optional array of molecular descriptor values. Defaults to None.

Raises

ValueError – Invalid file type specified.

Returns

Path to created file.

Return type

str

test_all_supported_measures()
test_get_abcd()
test_similarity_measure_limits()

tests.test_SimilarityMeasureValueErrors module

Test the ValueError exceptions in SimilarityMeasure

class tests.test_SimilarityMeasureValueErrors.TestSimilarityMeasureValueError(methodName='runTest')

Bases: TestCase

Tests for Value Error exception in SimilarityMeasure

test_binary_only_metrics()

Metrics which only allow bit vectors should raise a value error on other inputs.

test_compatible_metrics()

Test get_compatible_metrics basic functionailty.

test_empty_fprints()

Empty fingerprints cannot be compared.

test_invalid_metric()

Initializing with a non-existent metric should throw an error.

test_vectornorm_length_errors()

Vector norm-based similarities should only work with descriptors of the same length, otherwise it should raise a value error.

tests.test_TaskManager module

Test the TaskManager class.

class tests.test_TaskManager.TestTaskManager(methodName='runTest')

Bases: TestCase

classmethod setUpClass()

Hook method for setting up class fixture before running tests in the class.

test_no_tasks_task_manager()

Instant stop test for TaskManager class.

test_task_manager()

Complete run test for TaskManager class.

tests.test_ToolTip module

Test the ToolTip package (and all UI packages)

class tests.test_ToolTip.TestToolTip(methodName='runTest')

Bases: TestCase

Test the ToolTip package (and all UI packages) by importing them

test_import()

Attempt to import the UI app to ensure imports are correct

tests.test_multithreading module

Test multithreading to ensure consistent behavior with serial implementation.

class tests.test_multithreading.TestMultithreading(methodName='runTest')

Bases: TestCase

Unit tests to ensure consistency when running AIMSim as a single process or when using multiprocessing.

classmethod setUpClass()

Create a SMILES database to use for comparisons and find the similarity matrices and execution times.

classmethod tearDownClass()

Delete temporary files used in testing.

test_multithreading_autoconfig()

Ensure that MoleculeSet can automatically configure multiprocessing..

test_multithreading_consistency_10_threads()

Ensure that the similarity matrix produced with 10 threads is identical to that produced using a single thread and the serial implementation.

test_multithreading_consistency_2_threads()

Ensure that the similarity matrix produced with 2 threads is identical to that produced using a single thread and the serial implementation.

test_multithreading_consistency_3_threads()

Ensure that the similarity matrix produced with 3 threads is identical to that produced using a single thread and the serial implementation.

test_multithreading_consistency_4_threads()

Ensure that the similarity matrix produced with 4 threads is identical to that produced using a single thread and the serial implementation.

test_multithreading_consistency_5_threads()

Ensure that the similarity matrix produced with 5 threads is identical to that produced using a single thread and the serial implementation.

test_multithreading_consistency_6_threads()

Ensure that the similarity matrix produced with 6 threads is identical to that produced using a single thread and the serial implementation.

test_multithreading_consistency_7_threads()

Ensure that the similarity matrix produced with 7 threads is identical to that produced using a single thread and the serial implementation.

test_speedup_efficiency_cosine()

Evaluate the speedup and efficieny of the multiprocessing approach with a more complex metric.

test_speedup_efficiency_tanimoto()

Evaluate the speedup and efficieny of the multiprocessing approach.

Module contents