aimsim package

Subpackages

• aimsim.chemical_datastructures package
  • Submodules
  • aimsim.chemical_datastructures.molecule module
    • Molecule
      • Molecule.mol_graph
      • Molecule.mol_text
      • Molecule.mol_property_val
      • Molecule.descriptor
      • Molecule.get_descriptor_val()
      • Molecule.match_fingerprint_from()
      • Molecule.get_similarity_to()
      • Molecule.get_name()
      • Molecule.get_mol_property_val()
      • Molecule.draw()
      • Molecule.is_same()
      • Molecule.__init__()
      • Molecule.draw()
      • Molecule.get_descriptor_val()
      • Molecule.get_mol_property_val()
      • Molecule.get_name()
      • Molecule.get_similarity_to()
      • Molecule.is_same()
      • Molecule.match_fingerprint_from()
      • Molecule.set_descriptor()
  • aimsim.chemical_datastructures.molecule_set module
    • MoleculeSet
      • MoleculeSet.is_verbose
      • MoleculeSet.molecule_database
      • MoleculeSet.descriptor
      • MoleculeSet.similarity_measure
      • MoleculeSet.similarity_matrix
      • MoleculeSet.sampling_ratio
      • MoleculeSet.n_threads
      • MoleculeSet.is_present()
      • MoleculeSet.compare_against_molecule()
      • MoleculeSet.get_most_similar_pairs()
      • MoleculeSet.get_most_dissimilar_pairs()
      • MoleculeSet.get_property_of_most_similar()
      • MoleculeSet.get_property_of_most_dissimilar()
      • MoleculeSet.get_similarity_matrix()
      • MoleculeSet.get_distance_matrix()
      • MoleculeSet.get_pairwise_similarities()
      • MoleculeSet.get_mol_names()
      • MoleculeSet.get_mol_properties()
      • MoleculeSet.cluster()
      • MoleculeSet.get_cluster_labels()
      • MoleculeSet.get_transformed_descriptors()
      • MoleculeSet.__init__()
      • MoleculeSet.cluster()
      • MoleculeSet.compare_against_molecule()
      • MoleculeSet.get_cluster_labels()
      • MoleculeSet.get_distance_matrix()
      • MoleculeSet.get_mol_features()
      • MoleculeSet.get_mol_names()
      • MoleculeSet.get_mol_properties()
      • MoleculeSet.get_most_dissimilar_pairs()
      • MoleculeSet.get_most_similar_pairs()
      • MoleculeSet.get_pairwise_similarities()
      • MoleculeSet.get_property_of_most_dissimilar()
      • MoleculeSet.get_property_of_most_similar()
      • MoleculeSet.get_similarity_matrix()
      • MoleculeSet.get_transformed_descriptors()
      • MoleculeSet.is_present()
  • Module contents
• aimsim.ops package
  • Submodules
  • aimsim.ops.clustering module
    • Cluster
      • Cluster.n_clusters
      • Cluster.model_
      • Cluster.labels_
      • Cluster.fit()
      • Cluster.predict()
      • Cluster.get_labels()
      • Cluster.__init__()
      • Cluster.fit()
      • Cluster.get_labels()
      • Cluster.predict()
  • aimsim.ops.descriptor module
    • Descriptor
      • Descriptor.label_
      • Descriptor.numpy_
      • Descriptor.rdkit_
      • Descriptor.to_numpy()
      • Descriptor.to_rdkit()
      • Descriptor.check_init()
      • Descriptor.__init__()
      • Descriptor.check_init()
      • Descriptor.fold_to_equal_length()
      • Descriptor.get_all_supported_descriptors()
      • Descriptor.get_folded_fprint()
      • Descriptor.get_label()
      • Descriptor.get_params()
      • Descriptor.get_supported_fprints()
      • Descriptor.is_fingerprint()
      • Descriptor.make_fingerprint()
      • Descriptor.set_manually()
      • Descriptor.shorten_label()
      • Descriptor.to_numpy()
      • Descriptor.to_rdkit()
  • aimsim.ops.similarity_measures module
    • RegisteringType
      • RegisteringType.__init__()
    • SimilarityMeasure
      • SimilarityMeasure.__init__()
      • SimilarityMeasure.get_compatible_metrics()
      • SimilarityMeasure.get_supported_binary_metrics()
      • SimilarityMeasure.get_supported_general_metrics()
      • SimilarityMeasure.get_supported_metrics()
      • SimilarityMeasure.get_uniq_metrics()
      • SimilarityMeasure.is_distance_metric()
    • register()
  • Module contents
• aimsim.tasks package
  • Submodules
  • aimsim.tasks.cluster_data module
    • ClusterData
      • ClusterData.__init__()
  • aimsim.tasks.compare_target_molecule module
    • CompareTargetMolecule
      • CompareTargetMolecule.__init__()
      • CompareTargetMolecule.get_hits_dissimilar_to()
      • CompareTargetMolecule.get_hits_similar_to()
  • aimsim.tasks.extended_similarity_indices module
    • ExtendedSimilarityIndices
      • ExtendedSimilarityIndices.calculate_counters()
      • ExtendedSimilarityIndices.gen_sim_dict()
  • aimsim.tasks.identify_outliers module
    • IdentifyOutliers
      • IdentifyOutliers.__init__()
  • aimsim.tasks.measure_search module
    • MeasureSearch
      • MeasureSearch.__init__()
      • MeasureSearch.get_best_measure()
  • aimsim.tasks.see_property_variation_with_similarity module
    • SeePropertyVariationWithSimilarity
      • SeePropertyVariationWithSimilarity.__init__()
      • SeePropertyVariationWithSimilarity.get_property_correlations_in_most_dissimilar()
      • SeePropertyVariationWithSimilarity.get_property_correlations_in_most_similar()
  • aimsim.tasks.task module
    • Task
      • Task.__init__()
  • aimsim.tasks.task_manager module
    • TaskManager
      • TaskManager.__init__()
  • aimsim.tasks.visualize_dataset module
    • VisualizeDataset
      • VisualizeDataset.__init__()
  • Module contents
• aimsim.utils package
  • Submodules
  • aimsim.utils.ccbmlib_fingerprints module
    • atom_pairs()
    • avalon()
    • generate_fingerprints()
    • hash_parameter_set()
    • hashed_atom_pairs()
    • hashed_morgan()
    • hashed_torsions()
    • maccs_keys()
    • morgan()
    • rdkit_fingerprint()
    • to_key_val_string()
    • torsions()
  • aimsim.utils.plotting_scripts module
    • check_plot()
    • plot_barchart()
    • plot_density()
    • plot_heatmap()
    • plot_multiple_barchart()
    • plot_parity()
    • plot_scatter()
    • plot_scatter_interactive()
  • Module contents

Submodules

aimsim.exceptions module

exception aimsim.exceptions.InvalidConfigurationError(message=None)

Bases: OSError

Used when a configuration parameter is invalid.

__init__(message=None)

exception aimsim.exceptions.LoadingError(message=None)

Bases: ValueError

Used when an object cannot be loaded

__init__(message=None)

exception aimsim.exceptions.MordredCalculatorError(message=None)

Bases: RuntimeError

Used in descriptor.py when the Mordred property calculator fails.

__init__(message=None)

exception aimsim.exceptions.MordredNotInstalledWarning(message=None)

Bases: RuntimeWarning

Used in descriptor.py when the Mordred property calculator is not present.

__init__(message=None)

exception aimsim.exceptions.NotInitializedError(message=None)

Bases: AttributeError

Used when a class is called without proper initialization.

__init__(message=None)

Module contents