Index

A

atom_level_tokenizer (KmerSmilesTokenizer property)

AtomLevelSmilesTokenizer (class in deepmol.tokenizers.atom_level_smiles_tokenizer)

B

BaseFeatureSelector (class in deepmol.feature_selection.base_feature_selector) BaseScaler (class in deepmol.scalers.base_scaler) 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) ChEMBLStandardizer (class in deepmol.standardizer.chembl_standardizer) clear_cached_properties() (Dataset method) close_handlers() (Logger method) ClusterCentroids (class in deepmol.imbalanced_learn.imbalanced_learn) compute_metric() (Metric method)

compute_model_performance() (Evaluator method) compute_singletask_metric() (Metric method) create_handlers() (Logger method) critical() (Logger method) cross_validate() (DeepChemModel method) CustomStandardizer (class in deepmol.standardizer.custom_standardizer)

D

Dataset (class in deepmol.datasets.datasets) DatasetTransformer (class in deepmol.base.transformer) debug() (Logger method) DeepChemModel (class in deepmol.models.deepchem_models) deepmol module deepmol.base module deepmol.base.estimator module deepmol.base.predictor module deepmol.base.transformer module deepmol.datasets module deepmol.datasets.datasets module deepmol.encoders module deepmol.encoders.label_encoder module deepmol.encoders.label_one_hot_encoder module deepmol.evaluator module deepmol.evaluator.evaluator module deepmol.feature_selection module deepmol.feature_selection.base_feature_selector module deepmol.imbalanced_learn module deepmol.imbalanced_learn.imbalanced_learn module deepmol.loggers module deepmol.loggers.logger module deepmol.metrics module deepmol.metrics.metrics module deepmol.metrics.metrics_functions module deepmol.models.deepchem_models module deepmol.models.models module

deepmol.parallelism module deepmol.parallelism.multiprocessing module deepmol.scalers module deepmol.scalers.base_scaler module deepmol.scalers.sklearn_scalers module deepmol.splitters.multitask_splitter 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.tokenizers module deepmol.tokenizers.atom_level_smiles_tokenizer module deepmol.tokenizers.kmer_smiles_tokenizer module deepmol.tokenizers.tokenizer module deepmol.unsupervised module deepmol.unsupervised.base_unsupervised module deepmol.unsupervised.umap module deepmol.utils module deepmol.utils.cached_properties module deepmol.utils.decorators module deepmol.utils.errors module deepmol.utils.utils module deepmol_cached_property (class in deepmol.utils.cached_properties) disable() (Logger static method)

E

enable() (Logger method) encoder (LabelEncoder attribute) (LabelOneHotEncoder attribute) error() (Logger method)

Estimator (class in deepmol.base.estimator) evaluate() (DeepChemModel method) (Model method) (Predictor method) Evaluator (class in deepmol.evaluator.evaluator)

F

feature_names (Dataset property) (SmilesDataset property) fit() (DeepChemModel method) (Estimator method) (Predictor method)

fit_on_batch() (DeepChemModel method) (Model method) fit_transform() (Transformer method) from_mols() (SmilesDataset class method)

G

generate_scaffolds() (ScaffoldSplitter static method) generate_sequences() (in module deepmol.models.deepchem_models) get_class() (in module deepmol.utils.utils) get_model_filename() (Model static method) get_num_tasks() (DeepChemModel method) (Model method)

get_params_filename() (Model static method) get_shape() (Dataset method) (SmilesDataset method) get_task_type() (DeepChemModel method) (Model method)

I

ids (Dataset property) (SmilesDataset property) ImbalancedLearn (class in deepmol.imbalanced_learn.imbalanced_learn)

info() (Logger method) inplace_decorator() (in module deepmol.utils.decorators) is_fitted() (Estimator method) (Predictor method)

J

JoblibMultiprocessing (class in deepmol.parallelism.multiprocessing)

K

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

KbestFS (class in deepmol.feature_selection.base_feature_selector) KernelCenterer (class in deepmol.scalers.sklearn_scalers) KMeans (class in deepmol.unsupervised.base_unsupervised) KmerSmilesTokenizer (class in deepmol.tokenizers.kmer_smiles_tokenizer)

L

label_names (Dataset property) (SmilesDataset property) LabelEncoder (class in deepmol.encoders.label_encoder) LabelOneHotEncoder (class in deepmol.encoders.label_one_hot_encoder) load() (BaseScaler method) (DeepChemModel class method) (Model class method) (Predictor class 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

max_length (AtomLevelSmilesTokenizer property) (KmerSmilesTokenizer property) (Tokenizer property) MaxAbsScaler (class in deepmol.scalers.sklearn_scalers) merge() (SmilesDataset method) Metric (class in deepmol.metrics.metrics) MinMaxScaler (class in deepmol.scalers.sklearn_scalers) mode (Dataset property) (SmilesDataset property) Model (class in deepmol.models.models) model (DeepChemModel attribute) model_dir (Predictor property) model_type (DeepChemModel property) (Predictor property) modify_object_inplace_decorator() (in module deepmol.utils.decorators) module deepmol deepmol.base deepmol.base.estimator deepmol.base.predictor deepmol.base.transformer deepmol.datasets deepmol.datasets.datasets deepmol.encoders deepmol.encoders.label_encoder deepmol.encoders.label_one_hot_encoder deepmol.evaluator deepmol.evaluator.evaluator deepmol.feature_selection deepmol.feature_selection.base_feature_selector deepmol.imbalanced_learn deepmol.imbalanced_learn.imbalanced_learn deepmol.loggers deepmol.loggers.logger deepmol.metrics deepmol.metrics.metrics deepmol.metrics.metrics_functions deepmol.models.deepchem_models deepmol.models.models deepmol.parallelism deepmol.parallelism.multiprocessing deepmol.scalers deepmol.scalers.base_scaler deepmol.scalers.sklearn_scalers deepmol.splitters.multitask_splitter deepmol.splitters.splitters deepmol.standardizer deepmol.standardizer.basic_standardizer deepmol.standardizer.chembl_standardizer deepmol.standardizer.custom_standardizer deepmol.standardizer.molecular_standardizer deepmol.tokenizers deepmol.tokenizers.atom_level_smiles_tokenizer deepmol.tokenizers.kmer_smiles_tokenizer deepmol.tokenizers.tokenizer deepmol.unsupervised deepmol.unsupervised.base_unsupervised deepmol.unsupervised.umap deepmol.utils deepmol.utils.cached_properties deepmol.utils.decorators deepmol.utils.errors deepmol.utils.utils

mol_to_smiles() (in module deepmol.utils.utils) MolecularStandardizer (class in deepmol.standardizer.molecular_standardizer) mols (Dataset property) (SmilesDataset property) MultiprocessingClass (class in deepmol.parallelism.multiprocessing) MultiTaskStratifiedSplitter (class in deepmol.splitters.multitask_splitter)

N

n_tasks (Dataset property) (SmilesDataset property)

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

O

output_predictions() (Evaluator method)

output_statistics() (Evaluator static method)

P

PassThroughTransformer (class in deepmol.base.transformer) PCA (class in deepmol.unsupervised.base_unsupervised) pearson_score() (in module deepmol.metrics.metrics_functions) PercentilFS (class in deepmol.feature_selection.base_feature_selector) plot() (KMeans method) (PCA method) (TSNE method) (UMAP method) (UnsupervisedLearn method) plot_explained_variance() (PCA 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) (Model method) (Predictor method) predict_on_batch() (DeepChemModel method) (Model method) predict_proba() (DeepChemModel method) (Model method) (Predictor method) Predictor (class in deepmol.base.predictor) process (MultiprocessingClass property)

Q

QuantileTransformer (class in deepmol.scalers.sklearn_scalers)

R

RandomOverSampler (class in deepmol.imbalanced_learn.imbalanced_learn) RandomSplitter (class in deepmol.splitters.splitters) RandomUnderSampler (class in deepmol.imbalanced_learn.imbalanced_learn) regex (AtomLevelSmilesTokenizer property) (KmerSmilesTokenizer property) remove_duplicates() (SmilesDataset method) remove_elements() (Dataset method) (SmilesDataset method) remove_elements_by_index() (SmilesDataset method)

remove_nan() (Dataset method) (SmilesDataset method) removed_elements (Dataset property) (SmilesDataset property) RFECVFS (class in deepmol.feature_selection.base_feature_selector) RobustScaler (class in deepmol.scalers.sklearn_scalers) run() (JoblibMultiprocessing method) (MultiprocessingClass method) (UnsupervisedLearn method) run_iteratively() (MultiprocessingClass method)

S

sample() (ImbalancedLearn method) save() (BaseScaler method) (DeepChemModel method) (Model method) (Predictor method) save_features() (SmilesDataset method) ScaffoldSplitter (class in deepmol.splitters.splitters) scale() (BaseScaler method) scaler_object (BaseScaler property) 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) set_file_path() (Logger method) set_level() (Logger method) SimilaritySplitter (class in deepmol.splitters.splitters)

SingletaskStratifiedSplitter (class in deepmol.splitters.splitters) SingletonMeta (class in deepmol.loggers.logger) size (KmerSmilesTokenizer property) smiles (Dataset property) (SmilesDataset property) smiles_to_mol() (in module deepmol.utils.utils) SmilesDataset (class in deepmol.datasets.datasets) 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) split() (ButinaSplitter method) (MultiTaskStratifiedSplitter 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) stride (KmerSmilesTokenizer property)

T

timeout() (in module deepmol.utils.decorators) to_csv() (SmilesDataset method) to_dataframe() (SmilesDataset method) to_sdf() (SmilesDataset method) tokenize() (Tokenizer method) Tokenizer (class in deepmol.tokenizers.tokenizer)

tqdm_joblib() (in module deepmol.parallelism.multiprocessing) train_test_split() (Splitter method) train_valid_test_split() (Splitter method) transform() (Transformer method) Transformer (class in deepmol.base.transformer) TSNE (class in deepmol.unsupervised.base_unsupervised)

U

UMAP (class in deepmol.unsupervised.umap)

UnsupervisedLearn (class in deepmol.unsupervised.base_unsupervised)

V

vocabulary (AtomLevelSmilesTokenizer property) (KmerSmilesTokenizer property) (Tokenizer property)

W

warning() (Logger method)

X

X (Dataset property) (SmilesDataset attribute)

Y

y (Dataset property) (SmilesDataset property)