Index

A

All3DDescriptors (class in deepmol.compound_featurization.rdkit_descriptors) Asphericity (class in deepmol.compound_featurization.rdkit_descriptors)

AtomPairFingerprint (class in deepmol.compound_featurization.rdkit_fingerprints) AtomPairFingerprintCallbackHash (class in deepmol.compound_featurization.rdkit_fingerprints) AutoCorr3D (class in deepmol.compound_featurization.rdkit_descriptors)

B

BaseFeatureSelector (class in deepmol.feature_selection.base_feature_selector) BaseScaler (class in deepmol.scalers.base_scaler) basic_multitask_dnn() (in module deepmol.models.base_models)

BasicStandardizer (class in deepmol.standardizer.basic_standardizer) Binarizer (class in deepmol.scalers.sklearn_scalers) BorutaAlgorithm (class in deepmol.feature_selection.base_feature_selector) ButinaSplitter (class in deepmol.splitters.splitters)

C

canonicalize_mol_object() (in module deepmol.utils.utils) check_atoms_coordinates() (in module deepmol.compound_featurization.rdkit_descriptors) check_if_mol_has_explicit_hydrogens() (ThreeDimensionalMoleculeGenerator static method) ChEMBLStandardizer (class in deepmol.standardizer.chembl_standardizer) ClusterCentroids (class in deepmol.imbalanced_learn.imbalanced_learn) compute_metric() (Metric method) compute_model_performance() (Evaluator method) compute_singletask_metric() (Metric method) computeExactShap() (ShapValues method) computePermutationShap() (ShapValues method) ConvMolFeat (class in deepmol.compound_featurization.deepchem_featurizers)

CoulombEigFeat (class in deepmol.compound_featurization.deepchem_featurizers) CoulombFeat (class in deepmol.compound_featurization.deepchem_featurizers) create_dataset() (CSVLoader method) (SDFLoader method) create_dense_model() (in module deepmol.models.base_models) create_handlers() (Logger method) critical() (Logger method) cross_validate() (DeepChemModel method) (KerasModel method) (SklearnModel method) CSVLoader (class in deepmol.loaders.loaders) CustomStandardizer (class in deepmol.standardizer.custom_standardizer)

D

Dataset (class in deepmol.datasets.datasets) debug() (Logger method) DeepchemBaseSearchCV (class in deepmol.parameter_optimization.deepchem_hyperparameter_optimization) DeepchemGridSearchCV (class in deepmol.parameter_optimization.deepchem_hyperparameter_optimization) DeepChemModel (class in deepmol.models.deepchem_models) DeepchemRandomSearchCV (class in deepmol.parameter_optimization.deepchem_hyperparameter_optimization) deepmol module deepmol.compound_featurization module deepmol.compound_featurization.base_featurizer module deepmol.compound_featurization.deepchem_featurizers module deepmol.compound_featurization.mixed_descriptors module deepmol.compound_featurization.mol2vec module deepmol.compound_featurization.rdkit_descriptors module deepmol.compound_featurization.rdkit_fingerprints module deepmol.datasets module deepmol.datasets.datasets module deepmol.evaluator module deepmol.evaluator.evaluator module deepmol.feature_importance module deepmol.feature_importance.shap_values module deepmol.feature_selection module deepmol.feature_selection.base_feature_selector module deepmol.imbalanced_learn module deepmol.imbalanced_learn.imbalanced_learn module deepmol.loaders module deepmol.loaders.loaders module deepmol.loggers module deepmol.loggers.logger module deepmol.metrics module deepmol.metrics.metrics module deepmol.metrics.metrics_functions module deepmol.models module deepmol.models.base_models module

deepmol.models.deepchem_models module deepmol.models.ensembles module deepmol.models.keras_models module deepmol.models.models module deepmol.models.sklearn_models module deepmol.parallelism module deepmol.parallelism.multiprocessing module deepmol.parameter_optimization module deepmol.parameter_optimization.deepchem_hyperparameter_optimization module deepmol.parameter_optimization.hyperparameter_optimization module deepmol.scalers module deepmol.scalers.base_scaler module deepmol.scalers.sklearn_scalers module deepmol.splitters module deepmol.splitters.splitters module deepmol.standardizer module deepmol.standardizer.basic_standardizer module deepmol.standardizer.chembl_standardizer module deepmol.standardizer.custom_standardizer module deepmol.standardizer.molecular_standardizer module deepmol.unsupervised module deepmol.unsupervised.base_unsupervised module deepmol.unsupervised.umap module deepmol.utils module deepmol.utils.errors module deepmol.utils.utils module descriptor_function (ThreeDimensionDescriptor property) disable() (Logger static method) draw_MACCS_Pattern() (in module deepmol.utils.utils) draw_morgan_bit_on_molecule() (in module deepmol.utils.utils) draw_morgan_bits() (in module deepmol.utils.utils) draw_rdk_bit_on_molecule() (in module deepmol.utils.utils) draw_rdk_bits() (in module deepmol.utils.utils)

E

Eccentricity (class in deepmol.compound_featurization.rdkit_descriptors) enable() (Logger method) Ensemble (class in deepmol.models.ensembles) error() (Logger method)

evaluate() (DeepChemModel method) (Ensemble method) (Model method) Evaluator (class in deepmol.evaluator.evaluator)

F

feature_names (Dataset property) (SmilesDataset property) featurize() (MolecularFeaturizer method) (SmilesSeqFeat method) fit() (BaseScaler method) (DeepchemBaseSearchCV method) (DeepChemModel method) (Ensemble method) (KerasModel method) (Model method) (SklearnModel method)

fit_on_batch() (DeepChemModel method) (KerasModel method) (Model method) (SklearnModel method) fit_transform() (BaseScaler method) from_mols() (SmilesDataset class method)

G

generate_conformers() (in module deepmol.compound_featurization.rdkit_descriptors) (ThreeDimensionalMoleculeGenerator method) generate_conformers_to_sdf_file() (in module deepmol.compound_featurization.rdkit_descriptors) generate_descriptor() (ThreeDimensionDescriptor method) generate_scaffolds() (ScaffoldSplitter static method) generate_sequences() (in module deepmol.models.deepchem_models) get_all_3D_descriptors() (in module deepmol.compound_featurization.rdkit_descriptors) get_all_3D_descriptors_feature_names() (in module deepmol.compound_featurization.rdkit_descriptors) get_model_filename() (Model static method) get_num_tasks() (DeepChemModel method) (KerasModel method) (Model method) (SklearnModel method)

get_params_filename() (Model static method) get_shape() (Dataset method) (SmilesDataset method) get_task_type() (DeepChemModel method) (KerasModel method) (Model method) (SklearnModel method) getSubstructDepiction() (in module deepmol.utils.utils)

H

handler() (in module deepmol.compound_featurization.rdkit_descriptors) hash_function() (AtomPairFingerprintCallbackHash static method) hyperparameter_search() (HyperparameterOptimizer method) (HyperparameterOptimizerCV method) (HyperparameterOptimizerValidation method)

HyperparameterOptimizer (class in deepmol.parameter_optimization.hyperparameter_optimization) HyperparameterOptimizerCV (class in deepmol.parameter_optimization.hyperparameter_optimization) HyperparameterOptimizerValidation (class in deepmol.parameter_optimization.hyperparameter_optimization)

I

ids (Dataset property) (SmilesDataset property)

ImbalancedLearn (class in deepmol.imbalanced_learn.imbalanced_learn) InertialShapeFactor (class in deepmol.compound_featurization.rdkit_descriptors) info() (Logger method)

J

JoblibMultiprocessing (class in deepmol.parallelism.multiprocessing)

K

k_fold_split() (ButinaSplitter method) (RandomSplitter method) (ScaffoldSplitter method) (SimilaritySplitter method) (SingletaskStratifiedSplitter method) (Splitter method)

KbestFS (class in deepmol.feature_selection.base_feature_selector) KerasModel (class in deepmol.models.keras_models) KernelCenterer (class in deepmol.scalers.sklearn_scalers) KMeans (class in deepmol.unsupervised.base_unsupervised)

L

label_names (Dataset property) (SmilesDataset property) LayeredFingerprint (class in deepmol.compound_featurization.rdkit_fingerprints) load() (BaseScaler method) (Binarizer method) (KernelCenterer method) (MaxAbsScaler method) (MinMaxScaler method) (Normalizer method) (PolynomialFeatures method) (PowerTransformer method) (QuantileTransformer method) (RobustScaler method) (StandardScaler method)

load_features() (SmilesDataset method) load_from_disk() (in module deepmol.utils.utils) load_pickle_file() (in module deepmol.utils.utils) Logger (class in deepmol.loggers.logger) LowVarianceFS (class in deepmol.feature_selection.base_feature_selector)

M

MACCSkeysFingerprint (class in deepmol.compound_featurization.rdkit_fingerprints) make_cnn_model() (in module deepmol.models.base_models) MaxAbsScaler (class in deepmol.scalers.sklearn_scalers) merge() (SmilesDataset method) Metric (class in deepmol.metrics.metrics) MinMaxScaler (class in deepmol.scalers.sklearn_scalers) MixedFeaturizer (class in deepmol.compound_featurization.mixed_descriptors) mode (Dataset property) (SmilesDataset property) Model (class in deepmol.models.models) module deepmol deepmol.compound_featurization deepmol.compound_featurization.base_featurizer deepmol.compound_featurization.deepchem_featurizers deepmol.compound_featurization.mixed_descriptors deepmol.compound_featurization.mol2vec deepmol.compound_featurization.rdkit_descriptors deepmol.compound_featurization.rdkit_fingerprints deepmol.datasets deepmol.datasets.datasets deepmol.evaluator deepmol.evaluator.evaluator deepmol.feature_importance deepmol.feature_importance.shap_values deepmol.feature_selection deepmol.feature_selection.base_feature_selector deepmol.imbalanced_learn deepmol.imbalanced_learn.imbalanced_learn deepmol.loaders deepmol.loaders.loaders deepmol.loggers deepmol.loggers.logger deepmol.metrics deepmol.metrics.metrics deepmol.metrics.metrics_functions deepmol.models deepmol.models.base_models deepmol.models.deepchem_models deepmol.models.ensembles deepmol.models.keras_models deepmol.models.models deepmol.models.sklearn_models deepmol.parallelism deepmol.parallelism.multiprocessing deepmol.parameter_optimization deepmol.parameter_optimization.deepchem_hyperparameter_optimization deepmol.parameter_optimization.hyperparameter_optimization deepmol.scalers deepmol.scalers.base_scaler deepmol.scalers.sklearn_scalers deepmol.splitters deepmol.splitters.splitters deepmol.standardizer deepmol.standardizer.basic_standardizer deepmol.standardizer.chembl_standardizer deepmol.standardizer.custom_standardizer deepmol.standardizer.molecular_standardizer deepmol.unsupervised deepmol.unsupervised.base_unsupervised deepmol.unsupervised.umap deepmol.utils deepmol.utils.errors deepmol.utils.utils

Mol2Vec (class in deepmol.compound_featurization.mol2vec) mol_to_smiles() (in module deepmol.utils.utils) MolecularFeaturizer (class in deepmol.compound_featurization.base_featurizer) MolecularStandardizer (class in deepmol.standardizer.molecular_standardizer) MolGanFeat (class in deepmol.compound_featurization.deepchem_featurizers) MolGraphConvFeat (class in deepmol.compound_featurization.deepchem_featurizers) mols (Dataset property) (SmilesDataset property) moltosvg() (in module deepmol.utils.utils) MorganFingerprint (class in deepmol.compound_featurization.rdkit_fingerprints) MORSE (class in deepmol.compound_featurization.rdkit_descriptors) MultiprocessingClass (class in deepmol.parallelism.multiprocessing)

N

n_tasks (Dataset property) (SmilesDataset property)

normalize_labels_shape() (in module deepmol.utils.utils) NormalizedPrincipalMomentsRatios (class in deepmol.compound_featurization.rdkit_descriptors) Normalizer (class in deepmol.scalers.sklearn_scalers)

O

optimize_molecular_geometry() (ThreeDimensionalMoleculeGenerator method)

output_predictions() (Evaluator method) output_statistics() (Evaluator static method)

P

partial_fit() (BaseScaler method) (Binarizer method) (KernelCenterer method) (MaxAbsScaler method) (MinMaxScaler method) (Normalizer method) (PolynomialFeatures method) (PowerTransformer method) (QuantileTransformer method) (RobustScaler method) (StandardScaler method) PCA (class in deepmol.unsupervised.base_unsupervised) pearson_score() (in module deepmol.metrics.metrics_functions) PercentilFS (class in deepmol.feature_selection.base_feature_selector) PlaneOfBestFit (class in deepmol.compound_featurization.rdkit_descriptors) plot() (KMeans method) (PCA method) (TSNE method) (UMAP method) (UnsupervisedLearn method) plot_explained_variance() (PCA method)

plotFeatureExplanation() (ShapValues method) plotHeatMap() (ShapValues method) plotSampleExplanation() (ShapValues method) PolynomialFeatures (class in deepmol.scalers.sklearn_scalers) PowerTransformer (class in deepmol.scalers.sklearn_scalers) prc_auc_score() (in module deepmol.metrics.metrics_functions) PreConditionViolationException predict() (DeepChemModel method) (Ensemble method) (KerasModel method) (Model method) (SklearnModel method) (VotingClassifier method) predict_on_batch() (DeepChemModel method) (KerasModel method) (Model method) (SklearnModel method) predict_proba() (Model method) prepareMol() (in module deepmol.utils.utils) PrincipalMomentsOfInertia (class in deepmol.compound_featurization.rdkit_descriptors) process (MultiprocessingClass property)

Q

QuantileTransformer (class in deepmol.scalers.sklearn_scalers)

R

RadialDistributionFunction (class in deepmol.compound_featurization.rdkit_descriptors) RadiusOfGyration (class in deepmol.compound_featurization.rdkit_descriptors) RandomOverSampler (class in deepmol.imbalanced_learn.imbalanced_learn) RandomSplitter (class in deepmol.splitters.splitters) RandomUnderSampler (class in deepmol.imbalanced_learn.imbalanced_learn) RDKFingerprint (class in deepmol.compound_featurization.rdkit_fingerprints) reload() (DeepChemModel method) (KerasModel method) (Model method) (SklearnModel method) remove_duplicates() (SmilesDataset method)

remove_elements() (Dataset method) (SmilesDataset method) remove_elements_by_index() (SmilesDataset method) remove_nan() (Dataset method) (SmilesDataset method) rf_model_builder() (in module deepmol.models.base_models) RFECVFS (class in deepmol.feature_selection.base_feature_selector) RobustScaler (class in deepmol.scalers.sklearn_scalers) run() (JoblibMultiprocessing method) (MultiprocessingClass method) run_iteratively() (MultiprocessingClass method) run_unsupervised() (UnsupervisedLearn method)

S

sample() (ImbalancedLearn method) save() (BaseScaler method) (DeepChemModel method) (KerasModel method) (Model method) (SklearnModel method) save_features() (SmilesDataset method) ScaffoldSplitter (class in deepmol.splitters.splitters) scaler_object (BaseScaler property) (Binarizer property) (KernelCenterer property) (MaxAbsScaler property) (MinMaxScaler property) (Normalizer property) (PolynomialFeatures property) (PowerTransformer property) (QuantileTransformer property) (RobustScaler property) (StandardScaler property) SDFLoader (class in deepmol.loaders.loaders) select() (Dataset method) (SmilesDataset method) select_features() (BaseFeatureSelector method) select_features_by_index() (Dataset method) (SmilesDataset method) select_features_by_name() (Dataset method) (SmilesDataset method) select_to_split() (Dataset method) (SmilesDataset method)

SelectFromModelFS (class in deepmol.feature_selection.base_feature_selector) sentences2vec() (in module deepmol.compound_featurization.mol2vec) set_file_path() (Logger method) set_level() (Logger method) ShapValues (class in deepmol.feature_importance.shap_values) SimilaritySplitter (class in deepmol.splitters.splitters) SingletaskStratifiedSplitter (class in deepmol.splitters.splitters) SingletonMeta (class in deepmol.loggers.logger) SklearnModel (class in deepmol.models.sklearn_models) SmileImageFeat (class in deepmol.compound_featurization.deepchem_featurizers) smiles (Dataset property) (SmilesDataset property) smiles_to_mol() (in module deepmol.utils.utils) SmilesDataset (class in deepmol.datasets.datasets) SmilesSeqFeat (class in deepmol.compound_featurization.deepchem_featurizers) SMOTE (class in deepmol.imbalanced_learn.imbalanced_learn) SMOTEENN (class in deepmol.imbalanced_learn.imbalanced_learn) SMOTETomek (class in deepmol.imbalanced_learn.imbalanced_learn) spearman_score() (in module deepmol.metrics.metrics_functions) SpherocityIndex (class in deepmol.compound_featurization.rdkit_descriptors) split() (ButinaSplitter method) (RandomSplitter method) (ScaffoldSplitter method) (SimilaritySplitter method) (SingletaskStratifiedSplitter method) (Splitter method) Splitter (class in deepmol.splitters.splitters) standardize() (MolecularStandardizer method) StandardScaler (class in deepmol.scalers.sklearn_scalers) svm_model_builder() (in module deepmol.models.base_models)

T

ThreeDimensionalMoleculeGenerator (class in deepmol.compound_featurization.rdkit_descriptors) ThreeDimensionDescriptor (class in deepmol.compound_featurization.rdkit_descriptors) to_csv() (SmilesDataset method) train_test_split() (Splitter method)

train_valid_test_split() (Splitter method) transform() (BaseScaler method) TSNE (class in deepmol.unsupervised.base_unsupervised) TwoDimensionDescriptors (class in deepmol.compound_featurization.rdkit_descriptors)

U

UMAP (class in deepmol.unsupervised.umap)

UnsupervisedLearn (class in deepmol.unsupervised.base_unsupervised)

V

VotingClassifier (class in deepmol.models.ensembles)

W

warning() (Logger method)

WeaveFeat (class in deepmol.compound_featurization.deepchem_featurizers) WHIM (class in deepmol.compound_featurization.rdkit_descriptors)

X

X (Dataset property) (SmilesDataset property)

Y

y (Dataset property) (SmilesDataset property)