Index

_

__init__() (aimsim.chemical_datastructures.molecule.Molecule method) (aimsim.chemical_datastructures.molecule_set.MoleculeSet method) (aimsim.exceptions.InvalidConfigurationError method) (aimsim.exceptions.LoadingError method) (aimsim.exceptions.MordredCalculatorError method) (aimsim.exceptions.MordredNotInstalledWarning method) (aimsim.exceptions.NotInitializedError method) (aimsim.ops.clustering.Cluster method) (aimsim.ops.descriptor.Descriptor method) (aimsim.ops.similarity_measures.RegisteringType method) (aimsim.ops.similarity_measures.SimilarityMeasure method) (aimsim.tasks.cluster_data.ClusterData method) (aimsim.tasks.compare_target_molecule.CompareTargetMolecule method) (aimsim.tasks.identify_outliers.IdentifyOutliers method) (aimsim.tasks.measure_search.MeasureSearch method) (aimsim.tasks.see_property_variation_with_similarity.SeePropertyVariationWithSimilarity method) (aimsim.tasks.task.Task method) (aimsim.tasks.task_manager.TaskManager method) (aimsim.tasks.visualize_dataset.VisualizeDataset method) (interfaces.UI.AIMSim_ui_main.AIMSimUiApp method)

A

aimsim module aimsim.chemical_datastructures module aimsim.chemical_datastructures.molecule module aimsim.chemical_datastructures.molecule_set module aimsim.exceptions module aimsim.ops module aimsim.ops.clustering module aimsim.ops.descriptor module aimsim.ops.similarity_measures module aimsim.tasks module aimsim.tasks.cluster_data module aimsim.tasks.compare_target_molecule module

aimsim.tasks.extended_similarity_indices module aimsim.tasks.identify_outliers module aimsim.tasks.measure_search module aimsim.tasks.see_property_variation_with_similarity module aimsim.tasks.task module aimsim.tasks.task_manager module aimsim.tasks.visualize_dataset module aimsim.utils module aimsim.utils.ccbmlib_fingerprints module aimsim.utils.plotting_scripts module AIMSimUiApp (class in interfaces.UI.AIMSim_ui_main) atom_pairs() (in module aimsim.utils.ccbmlib_fingerprints) avalon() (in module aimsim.utils.ccbmlib_fingerprints)

B

browseCallback() (interfaces.UI.AIMSim_ui_main.AIMSimUiApp method)

C

calculate_counters() (aimsim.tasks.extended_similarity_indices.ExtendedSimilarityIndices method) check_init() (aimsim.ops.descriptor.Descriptor method), [1] check_plot() (in module aimsim.utils.plotting_scripts) Cluster (class in aimsim.ops.clustering)

cluster() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] ClusterData (class in aimsim.tasks.cluster_data) compare_against_molecule() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] CompareTargetMolecule (class in aimsim.tasks.compare_target_molecule)

D

descriptor (aimsim.chemical_datastructures.molecule.Molecule attribute) (aimsim.chemical_datastructures.molecule_set.MoleculeSet attribute)

Descriptor (class in aimsim.ops.descriptor) draw() (aimsim.chemical_datastructures.molecule.Molecule method), [1]

E

ExtendedSimilarityIndices (class in aimsim.tasks.extended_similarity_indices)

F

fit() (aimsim.ops.clustering.Cluster method), [1]

fold_to_equal_length() (aimsim.ops.descriptor.Descriptor static method)

G

gen_sim_dict() (aimsim.tasks.extended_similarity_indices.ExtendedSimilarityIndices method) generate_fingerprints() (in module aimsim.utils.ccbmlib_fingerprints) get_all_supported_descriptors() (aimsim.ops.descriptor.Descriptor static method) get_best_measure() (aimsim.tasks.measure_search.MeasureSearch method) get_cluster_labels() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_compatible_metrics() (aimsim.ops.similarity_measures.SimilarityMeasure static method) get_descriptor_val() (aimsim.chemical_datastructures.molecule.Molecule method), [1] get_distance_matrix() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_feature_set() (tests.test_MoleculeSet.TestMoleculeSet method) get_folded_fprint() (aimsim.ops.descriptor.Descriptor method) get_hits_dissimilar_to() (aimsim.tasks.compare_target_molecule.CompareTargetMolecule method) get_hits_similar_to() (aimsim.tasks.compare_target_molecule.CompareTargetMolecule method) get_label() (aimsim.ops.descriptor.Descriptor method) get_labels() (aimsim.ops.clustering.Cluster method), [1] get_mol_features() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method) get_mol_names() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_mol_properties() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1]

get_mol_property_val() (aimsim.chemical_datastructures.molecule.Molecule method), [1] get_most_dissimilar_pairs() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_most_similar_pairs() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_name() (aimsim.chemical_datastructures.molecule.Molecule method), [1] get_pairwise_similarities() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_params() (aimsim.ops.descriptor.Descriptor method) get_property_correlations_in_most_dissimilar() (aimsim.tasks.see_property_variation_with_similarity.SeePropertyVariationWithSimilarity method) get_property_correlations_in_most_similar() (aimsim.tasks.see_property_variation_with_similarity.SeePropertyVariationWithSimilarity method) get_property_of_most_dissimilar() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_property_of_most_similar() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_similarity_matrix() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_similarity_to() (aimsim.chemical_datastructures.molecule.Molecule method), [1] get_supported_binary_metrics() (aimsim.ops.similarity_measures.SimilarityMeasure static method) get_supported_fprints() (aimsim.ops.descriptor.Descriptor static method) get_supported_general_metrics() (aimsim.ops.similarity_measures.SimilarityMeasure static method) get_supported_metrics() (aimsim.ops.similarity_measures.SimilarityMeasure static method) get_transformed_descriptors() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] get_uniq_metrics() (aimsim.ops.similarity_measures.SimilarityMeasure static method)

H

hash_parameter_set() (in module aimsim.utils.ccbmlib_fingerprints) hashed_atom_pairs() (in module aimsim.utils.ccbmlib_fingerprints)

hashed_morgan() (in module aimsim.utils.ccbmlib_fingerprints) hashed_torsions() (in module aimsim.utils.ccbmlib_fingerprints) HEIGHT (interfaces.UI.AIMSim_ui_main.AIMSimUiApp attribute)

I

IdentifyOutliers (class in aimsim.tasks.identify_outliers) interfaces module interfaces.config_reader module interfaces.UI module interfaces.UI.AIMSim_ui_main module

InvalidConfigurationError is_distance_metric() (aimsim.ops.similarity_measures.SimilarityMeasure method) is_fingerprint() (aimsim.ops.descriptor.Descriptor method) is_present() (aimsim.chemical_datastructures.molecule_set.MoleculeSet method), [1] is_same() (aimsim.chemical_datastructures.molecule.Molecule method) (aimsim.chemical_datastructures.molecule.Molecule static method) is_verbose (aimsim.chemical_datastructures.molecule_set.MoleculeSet attribute)

L

label_ (aimsim.ops.descriptor.Descriptor attribute)

labels_ (aimsim.ops.clustering.Cluster attribute) LoadingError

M

maccs_keys() (in module aimsim.utils.ccbmlib_fingerprints) main() (in module interfaces.config_reader) (in module interfaces.UI.AIMSim_ui_main) make_fingerprint() (aimsim.ops.descriptor.Descriptor method) match_fingerprint_from() (aimsim.chemical_datastructures.molecule.Molecule method), [1] MeasureSearch (class in aimsim.tasks.measure_search) model_ (aimsim.ops.clustering.Cluster attribute) module aimsim aimsim.chemical_datastructures aimsim.chemical_datastructures.molecule aimsim.chemical_datastructures.molecule_set aimsim.exceptions aimsim.ops aimsim.ops.clustering aimsim.ops.descriptor aimsim.ops.similarity_measures aimsim.tasks aimsim.tasks.cluster_data aimsim.tasks.compare_target_molecule aimsim.tasks.extended_similarity_indices aimsim.tasks.identify_outliers aimsim.tasks.measure_search aimsim.tasks.see_property_variation_with_similarity aimsim.tasks.task aimsim.tasks.task_manager aimsim.tasks.visualize_dataset aimsim.utils aimsim.utils.ccbmlib_fingerprints aimsim.utils.plotting_scripts interfaces interfaces.config_reader interfaces.UI interfaces.UI.AIMSim_ui_main tests tests.test_CompareTargetMolecule tests.test_Descriptor tests.test_LoadingErrorException tests.test_MeasureSearch tests.test_Molecule tests.test_MoleculeSet tests.test_multithreading tests.test_SimilarityMeasure tests.test_SimilarityMeasureValueErrors tests.test_TaskManager tests.test_ToolTip

mol_graph (aimsim.chemical_datastructures.molecule.Molecule attribute) mol_property_val (aimsim.chemical_datastructures.molecule.Molecule attribute) mol_text (aimsim.chemical_datastructures.molecule.Molecule attribute) Molecule (class in aimsim.chemical_datastructures.molecule) molecule_database (aimsim.chemical_datastructures.molecule_set.MoleculeSet attribute) MoleculeSet (class in aimsim.chemical_datastructures.molecule_set) MordredCalculatorError MordredNotInstalledWarning morgan() (in module aimsim.utils.ccbmlib_fingerprints)

N

n_clusters (aimsim.ops.clustering.Cluster attribute) n_threads (aimsim.chemical_datastructures.molecule_set.MoleculeSet attribute)

NotInitializedError numpy_ (aimsim.ops.descriptor.Descriptor attribute)

O

openConfigCallback() (interfaces.UI.AIMSim_ui_main.AIMSimUiApp method)

P

plot_barchart() (in module aimsim.utils.plotting_scripts) plot_density() (in module aimsim.utils.plotting_scripts) plot_heatmap() (in module aimsim.utils.plotting_scripts) plot_multiple_barchart() (in module aimsim.utils.plotting_scripts)

plot_parity() (in module aimsim.utils.plotting_scripts) plot_scatter() (in module aimsim.utils.plotting_scripts) plot_scatter_interactive() (in module aimsim.utils.plotting_scripts) predict() (aimsim.ops.clustering.Cluster method), [1]

R

rdkit_ (aimsim.ops.descriptor.Descriptor attribute) rdkit_fingerprint() (in module aimsim.utils.ccbmlib_fingerprints) register() (in module aimsim.ops.similarity_measures)

RegisteringType (class in aimsim.ops.similarity_measures) run() (interfaces.UI.AIMSim_ui_main.AIMSimUiApp method) runCallback() (interfaces.UI.AIMSim_ui_main.AIMSimUiApp method)

S

sampling_ratio (aimsim.chemical_datastructures.molecule_set.MoleculeSet attribute) SeePropertyVariationWithSimilarity (class in aimsim.tasks.see_property_variation_with_similarity) set_descriptor() (aimsim.chemical_datastructures.molecule.Molecule method) set_manually() (aimsim.ops.descriptor.Descriptor method) setUpClass() (tests.test_multithreading.TestMultithreading class method) (tests.test_TaskManager.TestTaskManager class method) shorten_label() (aimsim.ops.descriptor.Descriptor static method) showAllDescriptorsCallback() (interfaces.UI.AIMSim_ui_main.AIMSimUiApp method) similarity_matrix (aimsim.chemical_datastructures.molecule_set.MoleculeSet attribute) similarity_measure (aimsim.chemical_datastructures.molecule_set.MoleculeSet attribute)

SimilarityMeasure (class in aimsim.ops.similarity_measures) smarts_seq_to_smiles_file() (tests.test_MoleculeSet.TestMoleculeSet method) smiles_seq_to_pdb_dir() (tests.test_MoleculeSet.TestMoleculeSet method) smiles_seq_to_smi_file() (tests.test_MoleculeSet.TestMoleculeSet method) smiles_seq_to_smiles_file() (tests.test_MoleculeSet.TestMoleculeSet method) smiles_seq_to_textfile() (tests.test_MeasureSearch.TestMeasureSearch method) (tests.test_MoleculeSet.TestMoleculeSet method) smiles_seq_to_xl_or_csv() (tests.test_CompareTargetMolecule.TestCompareTargetMolecule method) (tests.test_MoleculeSet.TestMoleculeSet method) (tests.test_SimilarityMeasure.TestSimilarityMeasure method)

T

Task (class in aimsim.tasks.task) TaskManager (class in aimsim.tasks.task_manager) tearDownClass() (tests.test_CompareTargetMolecule.TestCompareTargetMolecule class method) (tests.test_multithreading.TestMultithreading class method) test_all_supported_measures() (tests.test_SimilarityMeasure.TestSimilarityMeasure method) test_bad_descriptors_padelpy_descriptors() (tests.test_Descriptor.TestDescriptor method) test_binary_only_metrics() (tests.test_SimilarityMeasureValueErrors.TestSimilarityMeasureValueError method) test_ccbmlib_descriptors() (tests.test_Descriptor.TestDescriptor method) test_clustering_fingerprints() (tests.test_MoleculeSet.TestMoleculeSet method) test_compatible_metrics() (tests.test_SimilarityMeasureValueErrors.TestSimilarityMeasureValueError method) test_descriptor_arbitrary_list_init() (tests.test_Descriptor.TestDescriptor method) test_descriptor_arbitrary_numpy_init() (tests.test_Descriptor.TestDescriptor method) test_descriptor_empty_init() (tests.test_Descriptor.TestDescriptor method) test_descriptor_make_fingerprint() (tests.test_Descriptor.TestDescriptor method) test_empty_fprints() (tests.test_SimilarityMeasureValueErrors.TestSimilarityMeasureValueError method) test_error_optim_algo() (tests.test_MeasureSearch.TestMeasureSearch method) test_exptl_descriptors() (tests.test_Descriptor.TestDescriptor method) test_fingerprint_folding() (tests.test_Descriptor.TestDescriptor method) test_fixed_fprint() (tests.test_MeasureSearch.TestMeasureSearch method) test_fixed_SimilarityMeasure() (tests.test_MeasureSearch.TestMeasureSearch method) test_get_abcd() (tests.test_SimilarityMeasure.TestSimilarityMeasure method) test_get_molecule_least_similar_to() (tests.test_CompareTargetMolecule.TestCompareTargetMolecule method) test_get_molecule_most_similar_to() (tests.test_CompareTargetMolecule.TestCompareTargetMolecule method) test_get_most_dissimilar_pairs() (tests.test_MoleculeSet.TestMoleculeSet method) test_get_most_similar_pairs() (tests.test_MoleculeSet.TestMoleculeSet method) test_get_name() (tests.test_Molecule.TestMolecule method) test_get_property_value() (tests.test_Molecule.TestMolecule method) test_import() (tests.test_ToolTip.TestToolTip method) test_invalid_metric() (tests.test_SimilarityMeasureValueErrors.TestSimilarityMeasureValueError method) test_invalid_pdb() (tests.test_LoadingErrorException.TestLoadingERrorException method) test_invalid_smiles() (tests.test_LoadingErrorException.TestLoadingERrorException method) test_invalid_transform_error() (tests.test_MoleculeSet.TestMoleculeSet method) test_is_same() (tests.test_Molecule.TestMolecule method) test_isomap_transform() (tests.test_MoleculeSet.TestMoleculeSet method) test_logfile_generation() (tests.test_MeasureSearch.TestMeasureSearch method) test_match_fprint_error() (tests.test_Molecule.TestMolecule method) test_max_optim_algo() (tests.test_MeasureSearch.TestMeasureSearch method) test_mds_transform() (tests.test_MoleculeSet.TestMoleculeSet method) test_min_optim_algo() (tests.test_MeasureSearch.TestMeasureSearch method) test_minhash_fingerprint() (tests.test_Descriptor.TestDescriptor method) test_missing_pdb() (tests.test_LoadingErrorException.TestLoadingERrorException method) test_missing_smiles() (tests.test_LoadingErrorException.TestLoadingERrorException method) test_mol_mol_similarity_w_morgan_tanimoto() (tests.test_Molecule.TestMolecule method) test_mol_smiles_loadingerror() (tests.test_Molecule.TestMolecule method) test_mol_src_pdb_loadingerror() (tests.test_Molecule.TestMolecule method) test_mol_src_txt_loadingerror() (tests.test_Molecule.TestMolecule method) test_molecule_created_w_attributes() (tests.test_Molecule.TestMolecule method) test_molecule_created_with_no_attributes() (tests.test_Molecule.TestMolecule method) test_molecule_draw() (tests.test_Molecule.TestMolecule method) test_molecule_graph_similar_to_itself_morgan_dice() (tests.test_Molecule.TestMolecule method) test_molecule_graph_similar_to_itself_morgan_l0() (tests.test_Molecule.TestMolecule method) test_molecule_graph_similar_to_itself_morgan_tanimoto() (tests.test_Molecule.TestMolecule method) test_molecule_set_getters() (tests.test_MoleculeSet.TestMoleculeSet method) test_molecule_set_sim_getters() (tests.test_MoleculeSet.TestMoleculeSet method) test_mordred_descriptors() (tests.test_Descriptor.TestDescriptor method) test_msearch_completion() (tests.test_MeasureSearch.TestMeasureSearch method) test_msearch_init() (tests.test_MeasureSearch.TestMeasureSearch method) test_msearch_init_error() (tests.test_MeasureSearch.TestMeasureSearch method) test_multithreading_autoconfig() (tests.test_multithreading.TestMultithreading method) test_multithreading_consistency_10_threads() (tests.test_multithreading.TestMultithreading method) test_multithreading_consistency_2_threads() (tests.test_multithreading.TestMultithreading method) test_multithreading_consistency_3_threads() (tests.test_multithreading.TestMultithreading method) test_multithreading_consistency_4_threads() (tests.test_multithreading.TestMultithreading method) test_multithreading_consistency_5_threads() (tests.test_multithreading.TestMultithreading method) test_multithreading_consistency_6_threads() (tests.test_multithreading.TestMultithreading method) test_multithreading_consistency_7_threads() (tests.test_multithreading.TestMultithreading method) test_no_tasks_task_manager() (tests.test_TaskManager.TestTaskManager method) test_nonexistent_mordred_descriptors() (tests.test_Descriptor.TestDescriptor method) test_only_metric_fixed_fprint_search() (tests.test_MeasureSearch.TestMeasureSearch method) test_only_metric_fixed_measure_search() (tests.test_MeasureSearch.TestMeasureSearch method) test_only_metric_search() (tests.test_MeasureSearch.TestMeasureSearch method) test_padelpy_descriptors() (tests.test_Descriptor.TestDescriptor method) test_pca_transform() (tests.test_MoleculeSet.TestMoleculeSet method)

test_set_molecule_database_fingerprint_from_csv() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_from_csv() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_from_excel() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_from_excel_without_smiles_name() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_from_pdb_dir() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_from_smarts_file() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_from_smi_file() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_from_smiles_file() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_from_textfile() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_w_descriptor_property_from_csv() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_w_descriptor_property_from_excel() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_w_fingerprint_similarity_from_csv() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_w_property_from_csv() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_w_property_from_excel() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_w_property_from_textfile() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_database_w_similarity_from_csv() (tests.test_MoleculeSet.TestMoleculeSet method) test_set_molecule_from_file() (tests.test_Molecule.TestMolecule method) test_set_molecule_from_smiles() (tests.test_Molecule.TestMolecule method) test_similarity_measure_limits() (tests.test_SimilarityMeasure.TestSimilarityMeasure method) test_smarts (tests.test_MoleculeSet.TestMoleculeSet attribute) test_smiles (tests.test_MeasureSearch.TestMeasureSearch attribute) (tests.test_MoleculeSet.TestMoleculeSet attribute) test_spectral_embedding_transform() (tests.test_MoleculeSet.TestMoleculeSet method) test_speedup_efficiency_cosine() (tests.test_multithreading.TestMultithreading method) test_speedup_efficiency_tanimoto() (tests.test_multithreading.TestMultithreading method) test_subsample_molecule_database_from_csv() (tests.test_MoleculeSet.TestMoleculeSet method) test_subsample_molecule_database_from_excel() (tests.test_MoleculeSet.TestMoleculeSet method) test_subsample_molecule_database_from_pdb_dir() (tests.test_MoleculeSet.TestMoleculeSet method) test_subsample_molecule_database_from_textfile() (tests.test_MoleculeSet.TestMoleculeSet method) test_task_manager() (tests.test_TaskManager.TestTaskManager method) test_topological_fprint_min_path_lesser_than_atoms() (tests.test_Descriptor.TestDescriptor method) test_tsne_transform() (tests.test_MoleculeSet.TestMoleculeSet method) test_vectornorm_length_errors() (tests.test_SimilarityMeasureValueErrors.TestSimilarityMeasureValueError method) test_verbose_output() (tests.test_MeasureSearch.TestMeasureSearch method) TestCompareTargetMolecule (class in tests.test_CompareTargetMolecule) TestDescriptor (class in tests.test_Descriptor) TestLoadingERrorException (class in tests.test_LoadingErrorException) TestMeasureSearch (class in tests.test_MeasureSearch) TestMolecule (class in tests.test_Molecule) TestMoleculeSet (class in tests.test_MoleculeSet) TestMultithreading (class in tests.test_multithreading) tests module tests.test_CompareTargetMolecule module tests.test_Descriptor module tests.test_LoadingErrorException module tests.test_MeasureSearch module tests.test_Molecule module tests.test_MoleculeSet module tests.test_multithreading module tests.test_SimilarityMeasure module tests.test_SimilarityMeasureValueErrors module tests.test_TaskManager module tests.test_ToolTip module TestSimilarityMeasure (class in tests.test_SimilarityMeasure) TestSimilarityMeasureValueError (class in tests.test_SimilarityMeasureValueErrors) TestTaskManager (class in tests.test_TaskManager) TestToolTip (class in tests.test_ToolTip) to_key_val_string() (in module aimsim.utils.ccbmlib_fingerprints) to_numpy() (aimsim.ops.descriptor.Descriptor method), [1] to_rdkit() (aimsim.ops.descriptor.Descriptor method), [1] torsions() (in module aimsim.utils.ccbmlib_fingerprints)

U

useMeasureSearchCallback() (interfaces.UI.AIMSim_ui_main.AIMSimUiApp method)

V

VisualizeDataset (class in aimsim.tasks.visualize_dataset)

W

WIDTH (interfaces.UI.AIMSim_ui_main.AIMSimUiApp attribute)