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  • Applicability domain
    • BoundingBoxADChecker
    • ConvexHullADChecker
    • DistanceToCentroidADChecker
    • HotellingT2TestADChecker
    • LeverageADChecker
    • PCABoundingBoxADChecker
  • Base classes
    • BaseFilter
    • BaseFingerprintTransformer
    • BasePreprocessor
    • BaseSubstructureFingerprint
  • Datasets
    • Long Range Graph Benchmark (LRGB)
      • load_lrgb_mol_benchmark
      • load_lrgb_mol_splits
      • load_peptides_func
      • load_peptides_struct
    • MoleculeNet
      • load_moleculenet_benchmark
      • load_ogb_splits
      • load_bace
      • load_bbbp
      • load_clintox
      • load_esol
      • load_freesolv
      • load_hiv
      • load_lipophilicity
      • load_muv
      • load_pcba
      • load_sider
      • load_tox21
      • load_toxcast
    • TDC
      • load_tdc_benchmark
      • load_tdc_splits
      • load_b3db_classification
      • load_b3db_regression
      • load_bioavailability_ma
      • load_caco2_wang
      • load_clearance_hepatocyte_az
      • load_clearance_microsome_az
      • load_cyp1a2_veith
      • load_cyp2c19_veith
      • load_cyp2c9_substrate_carbonmangels
      • load_cyp2c9_veith
      • load_cyp2d6_substrate_carbonmangels
      • load_cyp2d6_veith
      • load_cyp3a4_substrate_carbonmangels
      • load_cyp3a4_veith
      • load_half_life_obach
      • load_hia_hou
      • load_hlm
      • load_pampa_approved_drugs
      • load_pampa_ncats
      • load_pgp_broccatelli
      • load_ppbr_az
      • load_rlm
      • load_solubility_aqsoldb
      • load_vdss_lombardo
      • load_sarscov2_3clpro_diamond
      • load_sarscov2_vitro_touret
      • load_ames
      • load_dili
      • load_carcinogens_lagunin
      • load_herg
      • load_herg_central_at_1um
      • load_herg_central_at_10um
      • load_herg_central_inhib
      • load_herg_karim
      • load_ld50_zhu
      • load_skin_reaction
  • Descriptors
    • atomic_partial_charges
    • average_molecular_weight
    • bond_count
    • element_atom_count
    • heavy_atom_count
    • molecular_weight
    • number_of_rings
    • number_of_rotatable_bonds
    • total_atom_count
    • average_wiener_index
    • balaban_j_index
    • burden_matrix
    • diameter
    • graph_distance_index
    • hall_kier_alpha
    • kappa1_index
    • kappa2_index
    • kappa3_index
    • petitjean_index
    • polarity_number
    • radius
    • wiener_index
    • zagreb_index_m1
    • zagreb_index_m2
  • Distances and similarities
    • braun_blanquet_binary_distance
    • ct4_binary_distance
    • ct4_count_distance
    • dice_binary_distance
    • dice_count_distance
    • fraggle_distance
    • harris_lahey_binary_distance
    • kulczynski_binary_distance
    • mcconnaughey_binary_distance
    • mcs_distance
    • rand_binary_distance
    • rogot_goldberg_binary_distance
    • russell_binary_distance
    • simpson_binary_distance
    • sokal_sneath_2_binary_distance
    • tanimoto_binary_distance
    • tanimoto_count_distance
    • bulk_braun_blanquet_binary_distance
    • bulk_ct4_binary_distance
    • bulk_ct4_count_distance
    • bulk_dice_binary_distance
    • bulk_dice_count_distance
    • bulk_fraggle_distance
    • bulk_harris_lahey_binary_distance
    • bulk_kulczynski_binary_distance
    • bulk_mcconnaughey_binary_distance
    • bulk_mcs_distance
    • bulk_rand_binary_distance
    • bulk_rogot_goldberg_binary_distance
    • bulk_russell_binary_distance
    • bulk_simpson_binary_distance
    • bulk_sokal_sneath_2_binary_distance
    • bulk_tanimoto_binary_distance
    • bulk_tanimoto_count_distance
    • braun_blanquet_binary_similarity
    • ct4_binary_similarity
    • ct4_count_similarity
    • dice_binary_similarity
    • dice_count_similarity
    • fraggle_similarity
    • harris_lahey_binary_similarity
    • kulczynski_binary_similarity
    • mcconnaughey_binary_similarity
    • mcs_similarity
    • rand_binary_similarity
    • rogot_goldberg_binary_similarity
    • russell_binary_similarity
    • simpson_binary_similarity
    • sokal_sneath_2_binary_similarity
    • tanimoto_binary_similarity
    • tanimoto_count_similarity
    • bulk_braun_blanquet_binary_similarity
    • bulk_ct4_binary_similarity
    • bulk_ct4_count_similarity
    • bulk_dice_binary_similarity
    • bulk_dice_count_similarity
    • bulk_fraggle_similarity
    • bulk_harris_lahey_binary_similarity
    • bulk_kulczynski_binary_similarity
    • bulk_mcconnaughey_binary_similarity
    • bulk_mcs_similarity
    • bulk_rand_binary_similarity
    • bulk_russell_binary_similarity
    • bulk_rogot_goldberg_binary_similarity
    • bulk_simpson_binary_similarity
    • bulk_sokal_sneath_2_binary_similarity
    • bulk_tanimoto_binary_similarity
    • bulk_tanimoto_count_similarity
  • Molecular filters
    • BeyondRo5Filter
    • BMSFilter
    • BrenkFilter
    • FAF4DruglikeFilter
    • FAF4LeadlikeFilter
    • GhoseFilter
    • GlaxoFilter
    • GSKFilter
    • HaoFilter
    • InpharmaticaFilter
    • LINTFilter
    • LipinskiFilter
    • MLSMRFilter
    • MolecularWeightFilter
    • NIBRFilter
    • NIHFilter
    • OpreaFilter
    • PAINSFilter
    • PfizerFilter
    • REOSFilter
    • RuleOfFourFilter
    • RuleOfThreeFilter
    • RuleOfTwoFilter
    • RuleOfVeberFilter
    • RuleOfXuFilter
    • SureChEMBLFilter
    • TiceHerbicidesFilter
    • TiceInsecticidesFilter
    • ValenceDiscoveryFilter
    • ZINCBasicFilter
    • ZINCDruglikeFilter
  • Fingerprints
    • AtomPairFingerprint
    • AutocorrFingerprint
    • AvalonFingerprint
    • BCUT2DFingerprint
    • E3FPFingerprint
    • ECFPFingerprint
    • ElectroShapeFingerprint
    • ERGFingerprint
    • EStateFingerprint
    • FunctionalGroupsFingerprint
    • GETAWAYFingerprint
    • GhoseCrippenFingerprint
    • KlekotaRothFingerprint
    • LaggnerFingerprint
    • LayeredFingerprint
    • LingoFingerprint
    • MACCSFingerprint
    • MAPFingerprint
    • MHFPFingerprint
    • MordredFingerprint
    • MORSEFingerprint
    • MQNsFingerprint
    • PatternFingerprint
    • PharmacophoreFingerprint
    • PhysiochemicalPropertiesFingerprint
    • PubChemFingerprint
    • RDFFingerprint
    • RDKitFingerprint
    • RDKit2DDescriptorsFingerprint
    • SECFPFingerprint
    • TopologicalTorsionFingerprint
    • USRFingerprint
    • USRCATFingerprint
    • VSAFingerprint
    • WHIMFingerprint
  • Metrics
    • auroc_score
    • spearman_correlation
    • multioutput_accuracy_score
    • multioutput_auprc_score
    • multioutput_auroc_score
    • multioutput_balanced_accuracy_score
    • multioutput_cohen_kappa_score
    • multioutput_f1_score
    • multioutput_matthews_corr_coef
    • multioutput_mean_absolute_error
    • multioutput_mean_squared_error
    • multioutput_precision_score
    • multioutput_recall_score
    • multioutput_root_mean_squared_error
    • multioutput_spearman_correlation
    • bedroc_score
    • enrichment_factor
    • rie_score
    • extract_pos_proba
  • Model selection
    • FingerprintEstimatorGridSearch
    • FingerprintEstimatorRandomizedSearch
    • butina_train_test_split
    • butina_train_valid_test_split
    • maxmin_train_test_split
    • maxmin_train_valid_test_split
    • randomized_scaffold_train_test_split
    • randomized_scaffold_train_valid_test_split
    • scaffold_train_test_split
    • scaffold_train_valid_test_split
  • Preprocessing
    • MolFromAminoseqTransformer
    • MolFromInchiTransformer
    • MolFromSDFTransformer
    • MolFromSmilesTransformer
    • MolToInchiTransformer
    • MolToSDFTransformer
    • MolToSmilesTransformer
    • ConformerGenerator
    • MolStandardizer
  • Utils
    • ensure_mols
    • ensure_smiles
    • require_mols
    • require_mols_with_conf_ids
    • require_strings
    • get_data_from_indices
    • no_rdkit_logs
    • run_in_parallel
  • API Reference
  • Base classes

Base classes#

Base classes for other functionalities. Inheriting from them is useful for implementing custom functionalities.


BaseFilter

Base class for molecular filters.

BaseFingerprintTransformer

Base class for fingerprints.

BasePreprocessor

Base class for preprocessing molecules.

BaseSubstructureFingerprint

Base class for substructure fingerprints.

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PCABoundingBoxADChecker

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BaseFilter

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