Index

A

accuracy() (in module qsarkit.metrics) accuracy_vs_coverage() (qsarkit.applicability.ADAnalyzer method) activities (qsarkit.data_quality.DuplicateGroup attribute) activity_a (qsarkit.sar.ActivityCliff attribute) activity_b (qsarkit.sar.ActivityCliff attribute) activity_check (qsarkit.data_quality.CurationReport attribute) activity_cliff_report() (in module qsarkit.sar) ActivityCliff (class in qsarkit.sar) ActivityCliffDetector (class in qsarkit.sar) ActivityLandscapePlotter (class in qsarkit.sar) ActivityOutlierDetector (class in qsarkit.data_quality) ADAnalyzer (class in qsarkit.applicability) add_applicability_section() (qsarkit.reporting.QSARReport method) add_dataset_section() (qsarkit.reporting.QSARReport method) add_evidence() (qsarkit.reporting.OECDReportBuilder method) add_model_section() (qsarkit.reporting.QSARReport method)

add_section() (qsarkit.reporting.QSARReport method) add_validation_section() (qsarkit.reporting.QSARReport method) adjusted_r2_score() (in module qsarkit.metrics) analyze() (qsarkit.chemspace.DiversityAnalyzer method) (qsarkit.explainability.FragmentContributionAnalyzer method) (qsarkit.sar.SARIAnalyzer method) applicability_domain() (in module qsarkit.functional) apply() (in module qsarkit.functional) atom_weights() (qsarkit.explainability.AttributionAtomMapper method) AtomicContribution (class in qsarkit.explainability) AtomicContributionMap (class in qsarkit.explainability) AtomPairFingerprint (class in qsarkit.representation) AttributionAtomMapper (class in qsarkit.explainability) available_metrics() (in module qsarkit.validation) AvalonFingerprint (class in qsarkit.representation) average_r2m() (in module qsarkit.metrics)

B

balance() (in module qsarkit.functional) balanced_accuracy() (in module qsarkit.metrics) BaseApplicabilityDomain (class in qsarkit.applicability) BaseDescriptorTransformer (class in qsarkit.representation) BaseFingerprintTransformer (class in qsarkit.representation) BaselineModel (class in qsarkit.models) BaseSplitter (class in qsarkit.model_selection) BaseUncertaintyEstimator (class in qsarkit.uncertainty) bedroc() (in module qsarkit.metrics) bemis_murcko() (qsarkit.chemistry.CoreExtractor method) bemis_murcko_smiles() (in module qsarkit.chemspace)

best_params_ (qsarkit.model_selection.NestedCV attribute) bias() (in module qsarkit.metrics) bit_atom_environments() (in module qsarkit.explainability) bit_weights_to_atom_weights() (in module qsarkit.explainability) BootstrapValidator (class in qsarkit.validation) BorutaSelector (class in qsarkit.feature_selection) BoundingBoxAD (in module qsarkit.applicability) brier_score() (in module qsarkit.metrics) build() (qsarkit.reporting.OECDReportBuilder method) (qsarkit.sar.SARTable method) ButinaClustering (class in qsarkit.cluster) ButinaClusterSplitter (class in qsarkit.model_selection)

C

calibration_curve() (in module qsarkit.metrics) calibration_report() (in module qsarkit.metrics) calibration_scores_ (qsarkit.uncertainty.ConformalClassifier attribute) (qsarkit.uncertainty.ConformalRegressor attribute) canonicalize_tautomers() (in module qsarkit.functional) ccc() (in module qsarkit.metrics) check_activity_units() (in module qsarkit.data_quality) check_mols() (in module qsarkit.utils) check_X_y_mols() (in module qsarkit.utils) ChemBERTaTransformer (class in qsarkit.representation) ChemicalSpaceAnalyzer (class in qsarkit.chemspace) ChemicalSpaceCoverage (class in qsarkit.chemspace) classes_ (qsarkit.models.QSARClassifier attribute) (qsarkit.neighbors.JaccardKNeighborsClassifier attribute) (qsarkit.uncertainty.ConformalClassifier attribute) cluster_centers_indices_ (qsarkit.cluster.ButinaClustering attribute) (qsarkit.cluster.SphereExclusionClustering attribute) cluster_members() (qsarkit.chemspace.ClusterAnalyzer method) ClusterAnalyzer (class in qsarkit.chemspace) code (qsarkit.data_quality.ValidationIssue attribute) cohen_kappa() (in module qsarkit.metrics) collect() (in module qsarkit.functional) collision_rate() (qsarkit.explainability.AttributionAtomMapper method) compare() (qsarkit.chemspace.ChemicalSpaceCoverage method) (qsarkit.chemspace.DiversityAnalyzer method)

compute() (qsarkit.explainability.PartialDependence method) compute_fingerprints() (in module qsarkit.chemspace) configure_logging() (in module qsarkit.utils) ConformalClassifier (class in qsarkit.uncertainty) ConformalPredictor() (in module qsarkit.uncertainty) ConformalRegressor (class in qsarkit.uncertainty) confusion_counts() (in module qsarkit.metrics) ConsensusModel (class in qsarkit.models) consistent (qsarkit.data_quality.DuplicateGroup attribute) ConstitutionalDescriptors (class in qsarkit.representation) content (qsarkit.reporting.ReportSection attribute) contributions_ (qsarkit.sar.FreeWilsonAnalysis attribute) convert_concentration() (in module qsarkit.utils) ConvexHullAD (class in qsarkit.applicability) core (qsarkit.sar.MatchedPair attribute) CoreExtractor (class in qsarkit.chemistry) correlation_matrix_ (qsarkit.feature_selection.CorrelationFilter attribute) CorrelationFilter (class in qsarkit.feature_selection) CounterfactualExplainer (class in qsarkit.explainability) coverage() (qsarkit.applicability.ADAnalyzer method) (qsarkit.applicability.BaseApplicabilityDomain method) coverage_curve() (qsarkit.uncertainty.UncertaintyCalibration method) created (qsarkit.persistence.ModelMetadata attribute) cross_validate() (in module qsarkit.functional) CrossValidator (class in qsarkit.validation) CurationReport (class in qsarkit.data_quality)

D

DataCurationPipeline (class in qsarkit.data_quality) dataframe_to_mols() (in module qsarkit.utils) decision_ (qsarkit.feature_selection.BorutaSelector attribute) decision_function() (qsarkit.applicability.BaseApplicabilityDomain method) decompose() (qsarkit.sar.RGroupAnalyzer method) DEFAULT_BIT_FLAGS (qsarkit.representation.AvalonFingerprint attribute) deglycate() (in module qsarkit.functional) delta (qsarkit.sar.ActivityCliff attribute) delta_activity (qsarkit.sar.MatchedPair attribute) delta_r2m() (in module qsarkit.metrics) desalt() (in module qsarkit.functional) describe() (in module qsarkit.functional) description (qsarkit.persistence.ModelMetadata attribute) DescriptorCalculator (class in qsarkit.representation) descriptors() (qsarkit.chemistry.MolecularGraph method) Descriptors3D (class in qsarkit.representation)

DescriptorScaler (class in qsarkit.transform) detail (qsarkit.functional.PipelineNode attribute) detect() (qsarkit.chemistry.GlycanDetector method) (qsarkit.data_quality.ActivityOutlierDetector method) (qsarkit.sar.ActivityCliffDetector method) diag() (qsarkit.models.TanimotoKernel method) DistanceToModelAD (class in qsarkit.applicability) DiversityAnalyzer (class in qsarkit.chemspace) domain (qsarkit.functional.PipelineNode attribute) draw_atom_weights() (in module qsarkit.explainability) drop_constant() (in module qsarkit.functional) drop_correlated() (in module qsarkit.functional) drop_if() (in module qsarkit.functional) drop_invalid() (in module qsarkit.functional) dummy_ (qsarkit.models.BaselineModel attribute) DuplicateDetector (class in qsarkit.data_quality) DuplicateGroup (class in qsarkit.data_quality)

E

embedding_ (qsarkit.chemspace.ChemicalSpaceAnalyzer attribute) ence() (qsarkit.uncertainty.UncertaintyCalibration method) endpoint (qsarkit.persistence.ModelMetadata attribute) enrichment_factor() (in module qsarkit.metrics) EnsembleAD (class in qsarkit.applicability) EnsembleUncertainty (class in qsarkit.uncertainty) ensure_mol_list() (in module qsarkit.base) environment (qsarkit.persistence.ModelMetadata attribute) environment_differences() (qsarkit.persistence.ModelMetadata method) environment_summary() (in module qsarkit.persistence) estimator_ (qsarkit.models.ConsensusModel attribute) (qsarkit.models.QSARClassifier attribute) (qsarkit.models.QSARRegressor attribute)

estimators_ (qsarkit.uncertainty.EnsembleUncertainty attribute) evaluate() (qsarkit.uncertainty.ConformalClassifier method) (qsarkit.uncertainty.ConformalRegressor method) (qsarkit.validation.CrossValidator method) expected_calibration_error() (in module qsarkit.metrics) explain() (qsarkit.explainability.AtomicContributionMap method) (qsarkit.explainability.CounterfactualExplainer method) explain_one() (qsarkit.explainability.LIMEExplainer method) (qsarkit.explainability.SHAPExplainer method) explainer (qsarkit.explainability.LIMEExplainer property) (qsarkit.explainability.SHAPExplainer property) ExternalValidator (class in qsarkit.validation) extra (qsarkit.persistence.ModelMetadata attribute)

F

f1_score() (in module qsarkit.metrics) fatal (qsarkit.data_quality.ValidationIssue attribute) feature_names (qsarkit.functional.FeatureSet attribute) (qsarkit.persistence.ModelMetadata attribute) feature_names_ (qsarkit.sar.FreeWilsonAnalysis attribute) feature_step() (in module qsarkit.functional) FeatureMorganFingerprint (class in qsarkit.representation) FeatureSet (class in qsarkit.functional) FeatureStep (class in qsarkit.functional) featurize() (in module qsarkit.functional) figure_to_html() (in module qsarkit.reporting) figures (qsarkit.reporting.ReportSection attribute) filter_by_property() (in module qsarkit.functional) find_duplicates() (qsarkit.data_quality.DuplicateDetector method) find_glycans() (qsarkit.chemistry.GlycanDetector method) find_pairs() (qsarkit.sar.MatchedMolecularPairs method) (qsarkit.sar.MMPAnalyzer method) fingerprint() (in module qsarkit.functional) FingerprintCombiner (class in qsarkit.representation) fingerprints_to_array() (in module qsarkit.chemspace) fit() (in module qsarkit.functional) (qsarkit.applicability.ADAnalyzer method) (qsarkit.applicability.BaseApplicabilityDomain method) (qsarkit.applicability.ConvexHullAD method) (qsarkit.applicability.DistanceToModelAD method) (qsarkit.applicability.EnsembleAD method) (qsarkit.applicability.IsolationForestAD method) (qsarkit.applicability.KernelDensityAD method) (qsarkit.applicability.KNNApplicabilityDomain method) (qsarkit.applicability.LeverageAD method) (qsarkit.applicability.PCABoundingBoxAD method) (qsarkit.applicability.RangeAD method) (qsarkit.applicability.TanimotoSimilarityAD method) (qsarkit.base.MoleculeTransformer method) (qsarkit.chemspace.ChemicalSpaceAnalyzer method) (qsarkit.chemspace.ClusterAnalyzer method) (qsarkit.chemspace.NearestNeighborAnalyzer method) (qsarkit.chemspace.ScaffoldAnalyzer method) (qsarkit.cluster.ButinaClustering method) (qsarkit.cluster.HierarchicalClustering method) (qsarkit.cluster.MaxMinPicker method) (qsarkit.cluster.SphereExclusionClustering method) (qsarkit.explainability.PermutationImportance method) (qsarkit.feature_selection.BorutaSelector method) (qsarkit.feature_selection.CorrelationFilter method) (qsarkit.feature_selection.MutualInformationSelector method) (qsarkit.feature_selection.RFESelector method) (qsarkit.feature_selection.VarianceFilter method) (qsarkit.models.BaselineModel method) (qsarkit.models.ConsensusModel method) (qsarkit.models.GaussianProcessQSAR method) (qsarkit.models.PLSRegressor method) (qsarkit.models.QSARClassifier method) (qsarkit.models.QSARRegressor method) (qsarkit.neighbors.JaccardKNeighborsClassifier method) (qsarkit.neighbors.JaccardKNeighborsRegressor method) (qsarkit.neighbors.JaccardNeighborSearch method) (qsarkit.representation.DescriptorCalculator method) (qsarkit.representation.FingerprintCombiner method) (qsarkit.representation.Mol2VecTransformer method) (qsarkit.sar.FreeWilsonAnalysis method) (qsarkit.transform.DescriptorScaler method) (qsarkit.transform.MoleculeFeatureUnion method) (qsarkit.transform.MolToSmiles method) (qsarkit.transform.NaNHandler method) (qsarkit.transform.SmilesToMol method) (qsarkit.transform.VarianceThresholdMol method) (qsarkit.uncertainty.BaseUncertaintyEstimator method) (qsarkit.uncertainty.ConformalClassifier method) (qsarkit.uncertainty.ConformalRegressor method) (qsarkit.uncertainty.EnsembleUncertainty method) (qsarkit.uncertainty.GaussianProcessUncertainty method) (qsarkit.uncertainty.MCDropoutUncertainty method) (qsarkit.uncertainty.QuantileRegressionUncertainty method)

fit_predict() (qsarkit.chemspace.ClusterAnalyzer method) (qsarkit.cluster.ButinaClustering method) (qsarkit.cluster.HierarchicalClustering method) (qsarkit.cluster.SphereExclusionClustering method) fit_transform() (qsarkit.chemspace.ChemicalSpaceAnalyzer method) (qsarkit.cluster.MaxMinPicker method) FittableMoleculeTransformer (class in qsarkit.base) fold_on_bits() (in module qsarkit.representation) format_version (qsarkit.persistence.ModelMetadata attribute) FragmentContributionAnalyzer (class in qsarkit.explainability) FragmentDescriptors (class in qsarkit.representation) FragmentRemover (class in qsarkit.chemistry) FreeWilsonAnalysis (class in qsarkit.sar) from_dict() (qsarkit.persistence.ModelMetadata class method) from_lime() (qsarkit.explainability.AttributionAtomMapper method) from_pactivity() (in module qsarkit.utils) from_pretrained() (qsarkit.representation.Mol2VecTransformer class method) from_shap() (qsarkit.explainability.AttributionAtomMapper method) from_validation() (qsarkit.reporting.OECDReportBuilder method) func (qsarkit.functional.FeatureStep attribute) (qsarkit.functional.Step attribute) (qsarkit.validation.Scorer attribute)

G

GaussianProcessQSAR (class in qsarkit.models) GaussianProcessUncertainty (class in qsarkit.uncertainty) get_feature_names_out() (qsarkit.representation.BaseDescriptorTransformer method) (qsarkit.representation.BaseFingerprintTransformer method) (qsarkit.representation.DescriptorCalculator method) (qsarkit.representation.FingerprintCombiner method) (qsarkit.representation.MACCSKeysFingerprint method) (qsarkit.representation.Mol2VecTransformer method) (qsarkit.transform.DescriptorScaler method) (qsarkit.transform.MoleculeFeatureUnion method) (qsarkit.transform.NaNHandler method)

get_logger() (in module qsarkit.utils) get_n_splits() (qsarkit.model_selection.BaseSplitter method) get_support() (qsarkit.transform.VarianceThresholdMol method) global_importance() (qsarkit.explainability.SHAPExplainer method) GlycanDescriptors (class in qsarkit.chemistry) GlycanDetector (class in qsarkit.chemistry) GlycanRemover (class in qsarkit.chemistry) golbraikh_tropsha_criteria() (in module qsarkit.metrics) greater_is_better (qsarkit.validation.Scorer attribute) groups() (qsarkit.chemspace.ScaffoldAnalyzer method)

H

HierarchicalClustering (class in qsarkit.cluster) history (qsarkit.functional.FeatureSet attribute) (qsarkit.functional.MoleculeSet attribute)

hits_ (qsarkit.feature_selection.BorutaSelector attribute) hyperparameter_search() (in module qsarkit.model_selection) hyperparameter_sigma_0 (qsarkit.models.TanimotoKernel property)

I

importances_mean_ (qsarkit.explainability.PermutationImportance attribute) importances_std_ (qsarkit.explainability.PermutationImportance attribute) impute() (in module qsarkit.functional) index (qsarkit.data_quality.ValidationIssue attribute) index_a (qsarkit.sar.ActivityCliff attribute) (qsarkit.sar.MatchedPair attribute) index_b (qsarkit.sar.ActivityCliff attribute) (qsarkit.sar.MatchedPair attribute) indices (qsarkit.data_quality.DuplicateGroup attribute) inspect_bundle() (in module qsarkit.persistence)

intercept_ (qsarkit.sar.FreeWilsonAnalysis attribute) interval_width() (qsarkit.uncertainty.ConformalRegressor method) InvalidMoleculeError inverse_transform() (qsarkit.transform.DescriptorScaler method) is_at_least_as_good_as() (qsarkit.validation.Scorer method) is_binary() (in module qsarkit.neighbors) is_fitted (qsarkit.base.FittableMoleculeTransformer property) is_stationary() (qsarkit.models.TanimotoKernel method) IsolationForestAD (class in qsarkit.applicability) iter_mols() (qsarkit.functional.MoleculeSet method)

J

jaccard_distance() (in module qsarkit.neighbors) jaccard_distance_matrix() (in module qsarkit.neighbors) jaccard_similarity() (in module qsarkit.neighbors)

JaccardKNeighborsClassifier (class in qsarkit.neighbors) JaccardKNeighborsRegressor (class in qsarkit.neighbors) JaccardNeighborSearch (class in qsarkit.neighbors)

K

k_prime_slope() (in module qsarkit.metrics) k_slope() (in module qsarkit.metrics) keep_if() (in module qsarkit.functional) KennardStoneSplitter (class in qsarkit.model_selection)

kernel (qsarkit.models.GaussianProcessQSAR attribute) KernelDensityAD (class in qsarkit.applicability) key (qsarkit.data_quality.DuplicateGroup attribute) kneighbors() (qsarkit.neighbors.JaccardNeighborSearch method) KNNApplicabilityDomain (class in qsarkit.applicability)

L

label (qsarkit.functional.PipelineNode attribute) labels_ (qsarkit.chemspace.ClusterAnalyzer attribute) (qsarkit.cluster.ButinaClustering attribute) (qsarkit.cluster.HierarchicalClustering attribute) (qsarkit.cluster.SphereExclusionClustering attribute)

LayeredFingerprint (class in qsarkit.representation) LeverageAD (class in qsarkit.applicability) LIMEExplainer (class in qsarkit.explainability) LipinskiDescriptors (class in qsarkit.representation) load() (qsarkit.persistence.ModelBundle class method) load_model() (in module qsarkit.persistence)

M

MACCSKeysFingerprint (class in qsarkit.representation) mae() (in module qsarkit.metrics) make_qsar_pipeline() (in module qsarkit.transform) make_scorer() (in module qsarkit.validation) MAP4Fingerprint (class in qsarkit.representation) MatchedMolecularPairs (class in qsarkit.sar) MatchedPair (class in qsarkit.sar) matthews_corrcoef() (in module qsarkit.metrics) maximum_calibration_error() (in module qsarkit.metrics) MaxMinPicker (class in qsarkit.cluster) MaxMinSplitter (class in qsarkit.model_selection) MCDropoutUncertainty (class in qsarkit.uncertainty) mcs() (qsarkit.chemistry.CoreExtractor method) medchem_core() (qsarkit.chemistry.CoreExtractor method) median_ae() (in module qsarkit.metrics) member_predictions() (qsarkit.applicability.EnsembleAD method) merge_replicates() (in module qsarkit.data_quality) message (qsarkit.data_quality.ValidationIssue attribute) method (qsarkit.validation.CrossValidator attribute) MHFPFingerprint (class in qsarkit.representation) min_distances_ (qsarkit.cluster.MaxMinPicker attribute) miscalibration_area() (qsarkit.uncertainty.UncertaintyCalibration method) missing_value (qsarkit.representation.BaseDescriptorTransformer attribute) MMPAnalyzer (class in qsarkit.sar) ModelBundle (class in qsarkit.persistence) ModelMetadata (class in qsarkit.persistence) ModelNotFittedError module qsarkit.applicability qsarkit.base qsarkit.chemistry qsarkit.chemspace qsarkit.cluster qsarkit.data_quality qsarkit.explainability qsarkit.feature_selection qsarkit.metrics qsarkit.model_selection qsarkit.models qsarkit.neighbors qsarkit.persistence qsarkit.reporting qsarkit.representation qsarkit.sar qsarkit.transform qsarkit.uncertainty qsarkit.utils qsarkit.validation

Mol2VecTransformer (class in qsarkit.representation) mol_a (qsarkit.sar.ActivityCliff attribute) (qsarkit.sar.MatchedPair attribute) mol_b (qsarkit.sar.ActivityCliff attribute) (qsarkit.sar.MatchedPair attribute) mol_to_sentence() (in module qsarkit.representation) MolecularGraph (class in qsarkit.chemistry) MolecularStandardizer (class in qsarkit.chemistry) MoleculeFeatureUnion (class in qsarkit.transform) molecules() (in module qsarkit.functional) MoleculeSet (class in qsarkit.functional) MoleculeToMoleculeTransformer (class in qsarkit.base) MoleculeTransformer (class in qsarkit.base) mols (qsarkit.functional.FeatureSet attribute) (qsarkit.functional.MoleculeSet attribute) mols_to_dataframe() (in module qsarkit.utils) MolToSmiles (class in qsarkit.transform) morgan_generator() (in module qsarkit.chemspace) MorganFingerprint (class in qsarkit.representation) most_common() (qsarkit.chemspace.ScaffoldAnalyzer method) most_negative (qsarkit.explainability.AtomicContribution property) most_positive (qsarkit.explainability.AtomicContribution property) mse() (in module qsarkit.metrics) MutualInformationSelector (class in qsarkit.feature_selection)

N

n_clusters_ (qsarkit.cluster.ButinaClustering attribute) (qsarkit.cluster.HierarchicalClustering attribute) (qsarkit.cluster.SphereExclusionClustering attribute) n_features (qsarkit.persistence.ModelMetadata attribute) n_features_in_ (qsarkit.applicability.BaseApplicabilityDomain attribute) (qsarkit.feature_selection.BorutaSelector attribute) (qsarkit.feature_selection.CorrelationFilter attribute) (qsarkit.feature_selection.MutualInformationSelector attribute) (qsarkit.feature_selection.RFESelector attribute) (qsarkit.feature_selection.VarianceFilter attribute) (qsarkit.neighbors.JaccardNeighborSearch attribute) (qsarkit.transform.DescriptorScaler attribute) (qsarkit.transform.NaNHandler attribute) (qsarkit.transform.VarianceThresholdMol attribute) n_features_out (qsarkit.representation.AtomPairFingerprint property) (qsarkit.representation.AvalonFingerprint property) (qsarkit.representation.BaseFingerprintTransformer property) (qsarkit.representation.LayeredFingerprint property) (qsarkit.representation.MACCSKeysFingerprint property) (qsarkit.representation.MAP4Fingerprint property) (qsarkit.representation.MHFPFingerprint property) (qsarkit.representation.MorganFingerprint property) (qsarkit.representation.PatternFingerprint property) (qsarkit.representation.PharmacophoreFingerprint property) (qsarkit.representation.RDKitFingerprint property) (qsarkit.representation.TopologicalTorsionFingerprint property)

n_input (qsarkit.data_quality.CurationReport attribute) n_output (qsarkit.data_quality.CurationReport attribute) n_removed (qsarkit.data_quality.CurationReport property) n_repeats (qsarkit.validation.CrossValidator attribute) n_scaffolds (qsarkit.chemspace.ScaffoldAnalyzer property) n_splits (qsarkit.validation.CrossValidator attribute) n_training_samples (qsarkit.persistence.ModelMetadata attribute) name (qsarkit.functional.PipeStep attribute) (qsarkit.persistence.ModelMetadata attribute) (qsarkit.validation.Scorer attribute) NaNHandler (class in qsarkit.transform) nearest_similarity() (qsarkit.chemspace.NearestNeighborAnalyzer method) NearestNeighborAnalyzer (class in qsarkit.chemspace) needs_proba (qsarkit.validation.Scorer attribute) NestedCV (class in qsarkit.model_selection) NeuralNetworkQSAR (class in qsarkit.models) neutralize() (in module qsarkit.functional) nm_to_molar() (in module qsarkit.utils) novelty() (qsarkit.chemspace.NearestNeighborAnalyzer method)

O

OECDReportBuilder (class in qsarkit.reporting)

optimal_threshold() (in module qsarkit.metrics) OptionalDependencyError

P

p_values() (qsarkit.uncertainty.ConformalClassifier method) pactivity_to_delta_g() (in module qsarkit.utils) params (qsarkit.functional.PipeStep attribute) PartialDependence (class in qsarkit.explainability) PatternFingerprint (class in qsarkit.representation) PCABoundingBoxAD (class in qsarkit.applicability) PerimeterSplitter (class in qsarkit.model_selection) PermutationImportance (class in qsarkit.explainability) PharmacophoreFingerprint (class in qsarkit.representation) PhysicochemicalDescriptors (class in qsarkit.representation) picks_ (qsarkit.cluster.MaxMinPicker attribute) pipeline() (in module qsarkit.functional) pipeline_nodes() (in module qsarkit.functional) PipelineNode (class in qsarkit.functional) PipeStep (class in qsarkit.functional) pivot() (qsarkit.sar.SARTable method) plot() (qsarkit.chemspace.ChemicalSpaceAnalyzer method) (qsarkit.explainability.AtomicContributionMap method) (qsarkit.explainability.PartialDependence method) (qsarkit.explainability.PermutationImportance method) (qsarkit.functional.FeatureSet method) (qsarkit.functional.MoleculeSet method) (qsarkit.functional.PipeStep method) (qsarkit.sar.ActivityLandscapePlotter method) (qsarkit.validation.YScrambling method) plot_accuracy_vs_coverage() (qsarkit.applicability.ADAnalyzer method) plot_atom_contributions() (in module qsarkit.reporting) plot_calibration() (qsarkit.uncertainty.UncertaintyCalibration method) plot_calibration_curve() (in module qsarkit.reporting) plot_feature_importance() (in module qsarkit.reporting) plot_importance() (qsarkit.explainability.SHAPExplainer method) plot_learning_curve() (in module qsarkit.reporting) plot_pipeline() (in module qsarkit.functional) plot_precision_recall() (in module qsarkit.reporting) plot_predicted_vs_observed() (in module qsarkit.reporting) plot_qq() (in module qsarkit.reporting)

plot_residuals() (in module qsarkit.reporting) plot_roc_curve() (in module qsarkit.reporting) plot_threshold_sweep() (in module qsarkit.reporting) plot_williams() (in module qsarkit.reporting) PLSRegressor (class in qsarkit.models) pr_auc() (in module qsarkit.metrics) precision() (in module qsarkit.metrics) predict() (qsarkit.applicability.BaseApplicabilityDomain method) (qsarkit.models.BaselineModel method) (qsarkit.models.ConsensusModel method) (qsarkit.models.QSARClassifier method) (qsarkit.models.QSARRegressor method) (qsarkit.neighbors.JaccardKNeighborsClassifier method) (qsarkit.neighbors.JaccardKNeighborsRegressor method) (qsarkit.persistence.ModelBundle method) (qsarkit.sar.FreeWilsonAnalysis method) (qsarkit.uncertainty.BaseUncertaintyEstimator method) (qsarkit.uncertainty.ConformalClassifier method) (qsarkit.uncertainty.ConformalRegressor method) predict_interval() (qsarkit.uncertainty.BaseUncertaintyEstimator method) (qsarkit.uncertainty.ConformalRegressor method) (qsarkit.uncertainty.QuantileRegressionUncertainty method) predict_mols() (qsarkit.persistence.ModelBundle method) predict_proba() (qsarkit.models.BaselineModel method) (qsarkit.models.ConsensusModel method) (qsarkit.models.QSARClassifier method) (qsarkit.neighbors.JaccardKNeighborsClassifier method) (qsarkit.persistence.ModelBundle method) predict_set() (qsarkit.uncertainty.ConformalClassifier method) predict_uncertainty() (qsarkit.uncertainty.BaseUncertaintyEstimator method) (qsarkit.uncertainty.EnsembleUncertainty method) (qsarkit.uncertainty.GaussianProcessUncertainty method) (qsarkit.uncertainty.MCDropoutUncertainty method) (qsarkit.uncertainty.QuantileRegressionUncertainty method) prediction (qsarkit.explainability.AtomicContribution attribute) press() (in module qsarkit.metrics) PRINCIPLES (qsarkit.reporting.OECDReportBuilder attribute)

Q

q2_f1() (in module qsarkit.metrics) q2_f2() (in module qsarkit.metrics) q2_f3() (in module qsarkit.metrics) qq_data() (in module qsarkit.metrics) qsar_classification_report() (in module qsarkit.metrics) qsar_regression_report() (in module qsarkit.metrics) QSARClassifier (class in qsarkit.models) qsarkit.applicability module qsarkit.base module qsarkit.chemistry module qsarkit.chemspace module qsarkit.cluster module qsarkit.data_quality module qsarkit.explainability module qsarkit.feature_selection module qsarkit.metrics module qsarkit.model_selection module

qsarkit.models module qsarkit.neighbors module qsarkit.persistence module qsarkit.reporting module qsarkit.representation module qsarkit.sar module qsarkit.transform module qsarkit.uncertainty module qsarkit.utils module qsarkit.validation module qsarkit_version (qsarkit.persistence.ModelMetadata attribute) QsarkitError QSARRegressor (class in qsarkit.models) QSARReport (class in qsarkit.reporting) quantile_ (qsarkit.uncertainty.ConformalRegressor attribute) QuantileRegressionUncertainty (class in qsarkit.uncertainty)

R

r0_prime_squared() (in module qsarkit.metrics) r0_squared() (in module qsarkit.metrics) r2_ (qsarkit.sar.FreeWilsonAnalysis attribute) r2_score() (in module qsarkit.metrics) r2m() (in module qsarkit.metrics) r2m_prime() (in module qsarkit.metrics) r_group_positions() (qsarkit.sar.RGroupAnalyzer method) radius_neighbors() (qsarkit.neighbors.JaccardNeighborSearch method) random_state (qsarkit.validation.CrossValidator attribute) RandomForestQSAR (class in qsarkit.models) RandomSplitter (class in qsarkit.model_selection) RangeAD (class in qsarkit.applicability) ranking_ (qsarkit.feature_selection.RFESelector attribute) RDKitDescriptors (class in qsarkit.representation) RDKitFingerprint (class in qsarkit.representation) read_csv_mols() (in module qsarkit.utils) read_sdf() (in module qsarkit.utils) read_smiles() (in module qsarkit.utils) real_score_ (qsarkit.validation.YScrambling attribute) recall() (in module qsarkit.metrics) redundancy() (qsarkit.chemspace.NearestNeighborAnalyzer method) remove() (qsarkit.chemistry.GlycanRemover method) remove_duplicates() (in module qsarkit.functional) remove_protecting_groups() (in module qsarkit.functional) removed (qsarkit.data_quality.CurationReport attribute)

render() (qsarkit.functional.FeatureSet method) (qsarkit.functional.MoleculeSet method) (qsarkit.functional.PipeStep method) render_pipeline() (in module qsarkit.functional) replace() (qsarkit.functional.FeatureSet method) (qsarkit.functional.MoleculeSet method) report() (qsarkit.applicability.ADAnalyzer method) (qsarkit.data_quality.DuplicateDetector method) (qsarkit.uncertainty.UncertaintyCalibration method) ReportSection (class in qsarkit.reporting) require() (in module qsarkit.base) resample() (in module qsarkit.functional) residual_normality() (in module qsarkit.metrics) residuals() (qsarkit.sar.FreeWilsonAnalysis method) retention (qsarkit.data_quality.CurationReport property) RFESelector (class in qsarkit.feature_selection) RGroupAnalyzer (class in qsarkit.sar) rmse() (in module qsarkit.metrics) rmsep() (in module qsarkit.metrics) robust_initial_enhancement() (in module qsarkit.metrics) roc_auc() (in module qsarkit.metrics) run() (qsarkit.data_quality.DataCurationPipeline method) (qsarkit.model_selection.NestedCV method) (qsarkit.validation.BootstrapValidator method) (qsarkit.validation.YScrambling method)

S

sali (qsarkit.sar.ActivityCliff attribute) sali_auc() (qsarkit.sar.SALIAnalyzer method) sali_curve() (qsarkit.sar.SALIAnalyzer method) sali_matrix() (qsarkit.sar.SALIAnalyzer method) sali_network() (qsarkit.sar.SALIAnalyzer method) SALIAnalyzer (class in qsarkit.sar) sample() (in module qsarkit.functional) SARIAnalyzer (class in qsarkit.sar) SARTable (class in qsarkit.sar) sas_data() (qsarkit.sar.ActivityLandscapePlotter method) save() (qsarkit.persistence.ModelBundle method) (qsarkit.representation.Mol2VecTransformer method) save_model() (in module qsarkit.persistence) ScaffoldAnalyzer (class in qsarkit.chemspace) scaffolds_ (qsarkit.chemspace.ScaffoldAnalyzer attribute) ScaffoldSplitter (class in qsarkit.model_selection) scale() (in module qsarkit.functional) scaler_ (qsarkit.transform.DescriptorScaler attribute) score() (qsarkit.models.BaselineModel method) (qsarkit.models.ConsensusModel method) score_samples() (qsarkit.applicability.BaseApplicabilityDomain method) (qsarkit.applicability.ConvexHullAD method) (qsarkit.applicability.DistanceToModelAD method) (qsarkit.applicability.EnsembleAD method) (qsarkit.applicability.IsolationForestAD method) (qsarkit.applicability.KernelDensityAD method) (qsarkit.applicability.KNNApplicabilityDomain method) (qsarkit.applicability.LeverageAD method) (qsarkit.applicability.PCABoundingBoxAD method) (qsarkit.applicability.RangeAD method) (qsarkit.applicability.TanimotoSimilarityAD method) Scorer (class in qsarkit.validation) scores() (qsarkit.data_quality.ActivityOutlierDetector method) scores_ (qsarkit.feature_selection.MutualInformationSelector attribute) (qsarkit.model_selection.NestedCV attribute) (qsarkit.validation.BootstrapValidator attribute) scrambled_scores_ (qsarkit.validation.YScrambling attribute) see() (in module qsarkit.metrics) select_features() (in module qsarkit.functional) sensitivity() (in module qsarkit.metrics) set_fit_request() (qsarkit.base.FittableMoleculeTransformer method) (qsarkit.base.MoleculeToMoleculeTransformer method) (qsarkit.base.MoleculeTransformer method) (qsarkit.chemistry.FragmentRemover method) (qsarkit.chemistry.GlycanDescriptors method) (qsarkit.chemistry.MolecularStandardizer method) (qsarkit.models.NeuralNetworkQSAR method) (qsarkit.models.RandomForestQSAR method) (qsarkit.models.SVMQSAR method) (qsarkit.representation.AtomPairFingerprint method) (qsarkit.representation.AvalonFingerprint method) (qsarkit.representation.BaseDescriptorTransformer method) (qsarkit.representation.BaseFingerprintTransformer method) (qsarkit.representation.ChemBERTaTransformer method) (qsarkit.representation.ConstitutionalDescriptors method) (qsarkit.representation.DescriptorCalculator method) (qsarkit.representation.Descriptors3D method) (qsarkit.representation.FeatureMorganFingerprint method) (qsarkit.representation.FingerprintCombiner method) (qsarkit.representation.FragmentDescriptors method) (qsarkit.representation.LayeredFingerprint method) (qsarkit.representation.LipinskiDescriptors method) (qsarkit.representation.MACCSKeysFingerprint method) (qsarkit.representation.MAP4Fingerprint method) (qsarkit.representation.MHFPFingerprint method) (qsarkit.representation.Mol2VecTransformer method) (qsarkit.representation.MorganFingerprint method) (qsarkit.representation.PatternFingerprint method) (qsarkit.representation.PharmacophoreFingerprint method) (qsarkit.representation.PhysicochemicalDescriptors method) (qsarkit.representation.RDKitDescriptors method) (qsarkit.representation.RDKitFingerprint method) (qsarkit.representation.TopologicalTorsionFingerprint method) set_partial_fit_request() (qsarkit.models.NeuralNetworkQSAR method) set_predict_request() (qsarkit.models.GaussianProcessQSAR method) (qsarkit.models.PLSRegressor method) set_score_request() (qsarkit.models.BaselineModel method) (qsarkit.models.ConsensusModel method) (qsarkit.models.GaussianProcessQSAR method) (qsarkit.models.NeuralNetworkQSAR method) (qsarkit.models.PLSRegressor method) (qsarkit.models.QSARClassifier method) (qsarkit.models.QSARRegressor method) (qsarkit.models.RandomForestQSAR method) (qsarkit.models.SVMQSAR method) (qsarkit.neighbors.JaccardKNeighborsClassifier method) (qsarkit.neighbors.JaccardKNeighborsRegressor method)

set_transform_request() (qsarkit.base.FittableMoleculeTransformer method) (qsarkit.base.MoleculeToMoleculeTransformer method) (qsarkit.base.MoleculeTransformer method) (qsarkit.chemistry.FragmentRemover method) (qsarkit.chemistry.GlycanDescriptors method) (qsarkit.chemistry.MolecularStandardizer method) (qsarkit.models.PLSRegressor method) (qsarkit.representation.AtomPairFingerprint method) (qsarkit.representation.AvalonFingerprint method) (qsarkit.representation.BaseDescriptorTransformer method) (qsarkit.representation.BaseFingerprintTransformer method) (qsarkit.representation.ChemBERTaTransformer method) (qsarkit.representation.ConstitutionalDescriptors method) (qsarkit.representation.DescriptorCalculator method) (qsarkit.representation.Descriptors3D method) (qsarkit.representation.FeatureMorganFingerprint method) (qsarkit.representation.FingerprintCombiner method) (qsarkit.representation.FragmentDescriptors method) (qsarkit.representation.LayeredFingerprint method) (qsarkit.representation.LipinskiDescriptors method) (qsarkit.representation.MACCSKeysFingerprint method) (qsarkit.representation.MAP4Fingerprint method) (qsarkit.representation.MHFPFingerprint method) (qsarkit.representation.Mol2VecTransformer method) (qsarkit.representation.MorganFingerprint method) (qsarkit.representation.PatternFingerprint method) (qsarkit.representation.PharmacophoreFingerprint method) (qsarkit.representation.PhysicochemicalDescriptors method) (qsarkit.representation.RDKitDescriptors method) (qsarkit.representation.RDKitFingerprint method) (qsarkit.representation.TopologicalTorsionFingerprint method) shap_values() (qsarkit.explainability.SHAPExplainer method) shape (qsarkit.functional.FeatureSet property) SHAPExplainer (class in qsarkit.explainability) shingles() (qsarkit.representation.MAP4Fingerprint method) shuffle() (in module qsarkit.functional) similarity (qsarkit.sar.ActivityCliff attribute) similarity_matrix() (qsarkit.sar.ActivityCliffDetector method) similarity_search() (qsarkit.neighbors.JaccardNeighborSearch method) similarity_to_training() (qsarkit.applicability.TanimotoSimilarityAD method) smiles (qsarkit.explainability.AtomicContribution attribute) (qsarkit.functional.MoleculeSet property) SmilesToMol (class in qsarkit.transform) spearman_error_correlation() (qsarkit.uncertainty.UncertaintyCalibration method) specificity() (in module qsarkit.metrics) SphereExclusionClustering (class in qsarkit.cluster) SphereExclusionSplitter (class in qsarkit.model_selection) split() (in module qsarkit.functional) (qsarkit.model_selection.BaseSplitter method) split_mols() (qsarkit.model_selection.BaseSplitter method) spread (qsarkit.data_quality.DuplicateGroup attribute) stages (qsarkit.data_quality.CurationReport attribute) standardize() (in module qsarkit.functional) statistics_ (qsarkit.transform.NaNHandler attribute) Step (class in qsarkit.functional) step() (in module qsarkit.functional) StratifiedScaffoldSplitter (class in qsarkit.model_selection) StructureValidator (class in qsarkit.data_quality) substituent_effects() (qsarkit.sar.SARTable method) summary() (qsarkit.chemspace.ClusterAnalyzer method) (qsarkit.chemspace.ScaffoldAnalyzer method) (qsarkit.data_quality.CurationReport method) support_ (qsarkit.feature_selection.BorutaSelector attribute) (qsarkit.feature_selection.CorrelationFilter attribute) (qsarkit.feature_selection.MutualInformationSelector attribute) (qsarkit.feature_selection.RFESelector attribute) (qsarkit.feature_selection.VarianceFilter attribute) (qsarkit.transform.NaNHandler attribute) (qsarkit.transform.VarianceThresholdMol attribute) SVMQSAR (class in qsarkit.models)

T

table (qsarkit.reporting.ReportSection attribute) tanimoto_matrix() (in module qsarkit.chemspace) tanimoto_similarity_matrix() (in module qsarkit.neighbors) TanimotoKernel (class in qsarkit.models) TanimotoSimilarityAD (class in qsarkit.applicability) task (qsarkit.persistence.ModelMetadata attribute) text (qsarkit.reporting.ReportSection attribute) threshold_ (qsarkit.applicability.BaseApplicabilityDomain attribute) threshold_report() (in module qsarkit.metrics) threshold_sweep() (in module qsarkit.metrics) TimeSplitter (class in qsarkit.model_selection) title (qsarkit.reporting.ReportSection attribute) to_dataframe() (qsarkit.chemspace.ScaffoldAnalyzer method) (qsarkit.data_quality.CurationReport method) (qsarkit.data_quality.DuplicateDetector method) (qsarkit.data_quality.StructureValidator method) (qsarkit.explainability.PermutationImportance method) (qsarkit.sar.ActivityCliffDetector method) (qsarkit.sar.FreeWilsonAnalysis method) (qsarkit.sar.MMPAnalyzer method) to_dict() (qsarkit.persistence.ModelMetadata method) (qsarkit.reporting.QSARReport method) (qsarkit.reporting.ReportSection method) to_dot() (in module qsarkit.functional) (qsarkit.functional.FeatureSet method) (qsarkit.functional.MoleculeSet method) (qsarkit.functional.PipeStep method)

to_frame() (qsarkit.functional.FeatureSet method) (qsarkit.functional.MoleculeSet method) to_html() (qsarkit.reporting.QSARReport method) to_json() (qsarkit.reporting.QSARReport method) to_markdown() (qsarkit.reporting.QSARReport method) to_networkx() (qsarkit.chemistry.MolecularGraph method) to_pactivity() (in module qsarkit.functional) (in module qsarkit.utils) to_pdf() (qsarkit.reporting.QSARReport method) to_similarity_map_weights() (qsarkit.explainability.AtomicContributionMap method) to_text() (qsarkit.reporting.QSARReport method) TopologicalTorsionFingerprint (class in qsarkit.representation) transform() (qsarkit.base.MoleculeTransformer method) (qsarkit.chemistry.CoreExtractor method) (qsarkit.chemistry.GlycanDetector method) (qsarkit.chemistry.GlycanRemover method) (qsarkit.chemistry.MolecularGraph method) (qsarkit.cluster.MaxMinPicker method) (qsarkit.explainability.AtomicContributionMap method) (qsarkit.transform.DescriptorScaler method) (qsarkit.transform.MoleculeFeatureUnion method) (qsarkit.transform.MolToSmiles method) (qsarkit.transform.NaNHandler method) (qsarkit.transform.SmilesToMol method) (qsarkit.transform.VarianceThresholdMol method) transformation (qsarkit.sar.MatchedPair attribute) transformation_summary() (qsarkit.sar.MMPAnalyzer method) transformers_ (qsarkit.transform.MoleculeFeatureUnion attribute)

U

unaddressed (qsarkit.reporting.OECDReportBuilder property)

UncertaintyCalibration (class in qsarkit.uncertainty)

V

valid_mask() (qsarkit.data_quality.StructureValidator method) validate() (qsarkit.data_quality.StructureValidator method) (qsarkit.validation.ExternalValidator method) ValidationIssue (class in qsarkit.data_quality)

VarianceFilter (class in qsarkit.feature_selection) variances_ (qsarkit.feature_selection.VarianceFilter attribute) (qsarkit.transform.VarianceThresholdMol attribute) VarianceThresholdMol (class in qsarkit.transform) vip_scores_ (qsarkit.models.PLSRegressor attribute)

W

warnings (qsarkit.data_quality.CurationReport attribute) weights (qsarkit.explainability.AtomicContribution attribute)

williams_plot() (qsarkit.applicability.ADAnalyzer method) write_sdf() (in module qsarkit.utils) write_smiles() (in module qsarkit.utils)

X

X (qsarkit.functional.FeatureSet attribute)

X_ (qsarkit.neighbors.JaccardNeighborSearch attribute)

Y

y (qsarkit.functional.FeatureSet attribute) (qsarkit.functional.MoleculeSet attribute)

YScrambling (class in qsarkit.validation)