deepmol package

Subpackages

• deepmol.base package
  • Submodules
  • deepmol.base.estimator module
    • Estimator
      • Estimator.fit()
      • Estimator.is_fitted()
  • deepmol.base.predictor module
    • Predictor
      • Predictor.evaluate()
      • Predictor.fit()
      • Predictor.is_fitted()
      • Predictor.load()
      • Predictor.model_dir
      • Predictor.model_type
      • Predictor.predict()
      • Predictor.predict_proba()
      • Predictor.save()
  • deepmol.base.transformer module
    • DatasetTransformer
    • PassThroughTransformer
    • Transformer
      • Transformer.fit_transform()
      • Transformer.transform()
  • Module contents
• deepmol.compound_featurization package
  • Subpackages
    • deepmol.compound_featurization.nc_mfp package
      • Submodules
      • deepmol.compound_featurization.nc_mfp.Fingerprint_representation_step module
      • deepmol.compound_featurization.nc_mfp.Fragment_identifying_step module
      • deepmol.compound_featurization.nc_mfp.Fragment_list_generation_step module
      • deepmol.compound_featurization.nc_mfp.Preprocessing_step module
      • deepmol.compound_featurization.nc_mfp.SFCP_assigning_step module
      • deepmol.compound_featurization.nc_mfp.Scaffold_matching_step module
      • deepmol.compound_featurization.nc_mfp.generate_database module
      • deepmol.compound_featurization.nc_mfp.identify_smarts_fragmets module
      • Module contents
    • deepmol.compound_featurization.neural_npfp package
      • Submodules
      • deepmol.compound_featurization.neural_npfp.model module
      • deepmol.compound_featurization.neural_npfp.utils module
      • Module contents
  • Submodules
  • deepmol.compound_featurization.base_featurizer module
  • deepmol.compound_featurization.deepchem_featurizers module
    • ConvMolFeat
      • ConvMolFeat.get_atom_features()
    • CoulombEigFeat
    • CoulombFeat
    • DMPNNFeat
    • DagTransformer
    • MATFeat
    • MolGanFeat
    • MolGraphConvFeat
    • PagtnMolGraphFeat
    • RawFeat
    • SmileImageFeat
    • SmilesSeqFeat
      • SmilesSeqFeat.featurize()
    • WeaveFeat
  • deepmol.compound_featurization.mhfp module
    • MHFP
  • deepmol.compound_featurization.mixed_descriptors module
    • MixedFeaturizer
  • deepmol.compound_featurization.mol2vec module
    • Mol2Vec
    • sentences2vec()
  • deepmol.compound_featurization.nc_mfp_generator module
    • NcMfp
      • NcMfp.generate_new_fingerprint_database()
  • deepmol.compound_featurization.neural_npfp_generator module
    • NeuralNPFP
  • deepmol.compound_featurization.np_classifier_fp module
    • NPClassifierFP
  • deepmol.compound_featurization.one_hot_encoder module
    • SmilesOneHotEncoder
      • SmilesOneHotEncoder.featurize()
      • SmilesOneHotEncoder.inverse_transform()
      • SmilesOneHotEncoder.shape
  • deepmol.compound_featurization.rdkit_descriptors module
    • All3DDescriptors
    • Asphericity
    • AutoCorr3D
    • Eccentricity
    • InertialShapeFactor
    • MORSE
    • NormalizedPrincipalMomentsRatios
    • PlaneOfBestFit
    • PrincipalMomentsOfInertia
    • RadialDistributionFunction
    • RadiusOfGyration
    • SpherocityIndex
    • ThreeDimensionDescriptor
      • ThreeDimensionDescriptor.descriptor_function
      • ThreeDimensionDescriptor.generate_descriptor()
    • ThreeDimensionalMoleculeGenerator
      • ThreeDimensionalMoleculeGenerator.check_if_mol_has_explicit_hydrogens()
      • ThreeDimensionalMoleculeGenerator.generate()
      • ThreeDimensionalMoleculeGenerator.generate_conformers()
      • ThreeDimensionalMoleculeGenerator.generate_structure()
      • ThreeDimensionalMoleculeGenerator.optimize_molecular_geometry()
    • TwoDimensionDescriptors
    • WHIM
    • check_atoms_coordinates()
    • generate_conformers()
    • generate_conformers_to_sdf_file()
    • get_all_3D_descriptors()
    • get_all_3D_descriptors_feature_names()
  • deepmol.compound_featurization.rdkit_fingerprints module
    • AtomPairFingerprint
    • AtomPairFingerprintCallbackHash
      • AtomPairFingerprintCallbackHash.hash_function()
    • LayeredFingerprint
    • MACCSkeysFingerprint
      • MACCSkeysFingerprint.draw_bit()
    • MorganFingerprint
      • MorganFingerprint.draw_bit()
      • MorganFingerprint.draw_bits()
    • RDKFingerprint
      • RDKFingerprint.draw_bit()
      • RDKFingerprint.draw_bits()
  • deepmol.compound_featurization.similarity_matrix module
    • TanimotoSimilarityMatrix
      • TanimotoSimilarityMatrix.featurize()
  • Module contents
• deepmol.datasets package
  • Submodules
  • deepmol.datasets.datasets module
    • Dataset
      • Dataset.X
      • Dataset.clear_cached_properties()
      • Dataset.feature_names
      • Dataset.get_shape()
      • Dataset.ids
      • Dataset.label_names
      • Dataset.mode
      • Dataset.mols
      • Dataset.n_tasks
      • Dataset.remove_elements()
      • Dataset.remove_nan()
      • Dataset.removed_elements
      • Dataset.select()
      • Dataset.select_features_by_index()
      • Dataset.select_features_by_name()
      • Dataset.select_to_split()
      • Dataset.smiles
      • Dataset.y
    • SmilesDataset
      • SmilesDataset.X
      • SmilesDataset.feature_names
      • SmilesDataset.from_mols()
      • SmilesDataset.get_shape()
      • SmilesDataset.ids
      • SmilesDataset.label_names
      • SmilesDataset.load_features()
      • SmilesDataset.merge()
      • SmilesDataset.mode
      • SmilesDataset.mols
      • SmilesDataset.n_tasks
      • SmilesDataset.remove_duplicates()
      • SmilesDataset.remove_elements()
      • SmilesDataset.remove_elements_by_index()
      • SmilesDataset.remove_nan()
      • SmilesDataset.removed_elements
      • SmilesDataset.save_features()
      • SmilesDataset.select()
      • SmilesDataset.select_features_by_index()
      • SmilesDataset.select_features_by_name()
      • SmilesDataset.select_to_split()
      • SmilesDataset.smiles
      • SmilesDataset.to_csv()
      • SmilesDataset.to_dataframe()
      • SmilesDataset.to_sdf()
      • SmilesDataset.y
  • Module contents
• deepmol.encoders package
  • Submodules
  • deepmol.encoders.label_encoder module
    • LabelEncoder
      • LabelEncoder.encoder
  • deepmol.encoders.label_one_hot_encoder module
    • LabelOneHotEncoder
      • LabelOneHotEncoder.encoder
  • Module contents
• deepmol.evaluator package
  • Submodules
  • deepmol.evaluator.evaluator module
    • Evaluator
      • Evaluator.compute_model_performance()
      • Evaluator.output_predictions()
      • Evaluator.output_statistics()
  • Module contents
• deepmol.feature_importance package
  • Submodules
  • deepmol.feature_importance.shap_values module
    • ShapValues
      • ShapValues.bar_plot()
      • ShapValues.beeswarm_plot()
      • ShapValues.decision_plot()
      • ShapValues.feature_explanation_plot()
      • ShapValues.fit()
      • ShapValues.heatmap_plot()
      • ShapValues.negative_class_plot()
      • ShapValues.positive_class_plot()
      • ShapValues.sample_explanation_plot()
  • Module contents
• deepmol.feature_selection package
  • Submodules
  • deepmol.feature_selection.base_feature_selector module
    • BaseFeatureSelector
      • BaseFeatureSelector.select_features()
    • BorutaAlgorithm
    • KbestFS
    • LowVarianceFS
    • PercentilFS
    • RFECVFS
    • SelectFromModelFS
  • Module contents
• deepmol.imbalanced_learn package
  • Submodules
  • deepmol.imbalanced_learn.imbalanced_learn module
    • ClusterCentroids
    • ImbalancedLearn
      • ImbalancedLearn.sample()
    • RandomOverSampler
    • RandomUnderSampler
    • SMOTE
    • SMOTEENN
    • SMOTETomek
  • Module contents
• deepmol.loaders package
  • Submodules
  • deepmol.loaders.loaders module
    • CSVLoader
      • CSVLoader.create_dataset()
    • SDFLoader
      • SDFLoader.create_dataset()
  • Module contents
• deepmol.loggers package
  • Submodules
  • deepmol.loggers.logger module
    • Logger
      • Logger.close_handlers()
      • Logger.create_handlers()
      • Logger.critical()
      • Logger.debug()
      • Logger.disable()
      • Logger.enable()
      • Logger.error()
      • Logger.info()
      • Logger.set_file_path()
      • Logger.set_level()
      • Logger.warning()
    • SingletonMeta
  • Module contents
• deepmol.metrics package
  • Submodules
  • deepmol.metrics.metrics module
    • Metric
      • Metric.compute_metric()
      • Metric.compute_singletask_metric()
  • deepmol.metrics.metrics_functions module
    • pearson_score()
    • prc_auc_score()
    • spearman_score()
  • Module contents
• deepmol.models package
  • Submodules
  • deepmol.models.base_models module
    • basic_multitask_dnn()
    • create_dense_model()
    • make_cnn_model()
    • rf_model_builder()
    • svm_model_builder()
  • deepmol.models.deepchem_model_builders module
    • attentivefp_model()
    • check_if_cuda_is_available_for_dgl()
    • chem_ception_model()
    • cnn_model()
    • dag_model()
    • dmpnn_model()
    • dtnn_model()
    • gat_model()
    • gcn_model()
    • graph_conv_model()
    • mat_model()
    • megnet_model()
    • mpnn_model()
    • multitask_classifier_model()
    • multitask_irv_classifier_model()
    • multitask_regressor_model()
    • pagtn_model()
    • progressive_multitask_classifier_model()
    • progressive_multitask_regressor_model()
    • robust_multitask_classifier_model()
    • robust_multitask_regressor_model()
    • sc_score_model()
    • smiles_to_vec_model()
    • text_cnn_model()
    • weave_model()
  • deepmol.models.deepchem_models module
    • DeepChemModel
      • DeepChemModel.cross_validate()
      • DeepChemModel.evaluate()
      • DeepChemModel.fit()
      • DeepChemModel.fit_on_batch()
      • DeepChemModel.get_num_tasks()
      • DeepChemModel.get_task_type()
      • DeepChemModel.load()
      • DeepChemModel.model
      • DeepChemModel.model_type
      • DeepChemModel.predict()
      • DeepChemModel.predict_on_batch()
      • DeepChemModel.predict_proba()
      • DeepChemModel.save()
    • generate_sequences()
  • deepmol.models.ensembles module
    • Ensemble
      • Ensemble.evaluate()
      • Ensemble.fit()
      • Ensemble.predict()
    • VotingClassifier
      • VotingClassifier.predict()
  • deepmol.models.keras_model_builders module
    • keras_1d_cnn_model()
    • keras_1d_cnn_model_builder()
    • keras_bidirectional_rnn_model()
    • keras_bidirectional_rnn_model_builder()
    • keras_fcnn_model()
    • keras_fcnn_model_builder()
    • keras_rnn_model()
    • keras_rnn_model_builder()
    • keras_simple_rnn_model()
    • keras_simple_rnn_model_builder()
    • keras_tabular_transformer_model()
    • keras_tabular_transformer_model_builder()
  • deepmol.models.keras_models module
    • KerasModel
      • KerasModel.cross_validate()
      • KerasModel.fit_on_batch()
      • KerasModel.get_num_tasks()
      • KerasModel.get_task_type()
      • KerasModel.load()
      • KerasModel.model_type
      • KerasModel.predict()
      • KerasModel.predict_on_batch()
      • KerasModel.predict_proba()
      • KerasModel.save()
  • deepmol.models.models module
    • Model
      • Model.evaluate()
      • Model.fit_on_batch()
      • Model.get_model_filename()
      • Model.get_num_tasks()
      • Model.get_params_filename()
      • Model.get_task_type()
      • Model.load()
      • Model.predict()
      • Model.predict_on_batch()
      • Model.predict_proba()
      • Model.save()
  • deepmol.models.sklearn_model_builders module
    • ada_boost_classifier_model()
    • ada_boost_regressor_model()
    • ard_regression_model()
    • bagging_classifier_model()
    • bagging_regressor_model()
    • bayesian_ridge_model()
    • bernoulli_nb_model()
    • categorical_nb_model()
    • classifier_chain_model()
    • complement_nb_model()
    • decision_tree_classifier_model()
    • decision_tree_regressor_model()
    • elastic_net_model()
    • extra_tree_classifier_model()
    • extra_tree_regressor_model()
    • extra_trees_classifier_model()
    • extra_trees_regressor_model()
    • gamma_regressor_model()
    • gaussian_nb_model()
    • gaussian_process_classifier_model()
    • gaussian_process_regressor_model()
    • gradient_boosting_classifier_model()
    • gradient_boosting_regressor_model()
    • hist_gradient_boosting_classifier_model()
    • hist_gradient_boosting_regressor_model()
    • huber_regressor_model()
    • isotonic_regression_model()
    • kernel_ridge_regressor_model()
    • kneighbors_classifier_model()
    • kneighbors_regressor_model()
    • label_propagation_model()
    • label_spreading_model()
    • lasso_cv_model()
    • lasso_lars_cv_model()
    • lasso_lars_ic_model()
    • lasso_model()
    • linear_discriminant_analysis_model()
    • linear_regression_model()
    • linear_svc_model()
    • linear_svr_model()
    • logistic_regression_cv_model()
    • logistic_regression_model()
    • mlp_classifier_model()
    • mlp_regressor_model()
    • multi_output_classifier_model()
    • multi_output_regressor_model()
    • multinomial_nb_model()
    • multitask_elastic_net_cv_model()
    • multitask_elastic_net_model()
    • multitask_lasso_model()
    • nearest_centroid_model()
    • nu_svc_model()
    • nu_svr_model()
    • one_class_svm_model()
    • one_vs_one_classifier_model()
    • one_vs_rest_classifier_model()
    • ortogonal_matching_pursuit_model()
    • output_code_classifier_model()
    • passive_aggressive_classifier_model()
    • passive_aggressive_regressor_model()
    • perceptron_model()
    • pls_regression_model()
    • poisson_regressor_model()
    • quadratic_discriminant_analysis_model()
    • quantile_regressor_model()
    • radius_neighbors_classifier_model()
    • radius_neighbors_regressor_model()
    • random_forest_classifier_model()
    • random_forest_regressor_model()
    • ransac_regressor_model()
    • regressor_chain_model()
    • ridge_classifier_cv_model()
    • ridge_classifier_model()
    • ridge_cv_model()
    • ridge_model()
    • sgd_classifier_model()
    • sgd_one_class_svm_model()
    • sgd_regressor_model()
    • stacking_classifier_model()
    • stacking_regressor_model()
    • svc_model()
    • svr_model()
    • theil_sen_regressor_model()
    • tweedie_regressor_model()
    • voting_classifier_model()
    • voting_regressor_model()
  • deepmol.models.sklearn_models module
    • SklearnModel
      • SklearnModel.cross_validate()
      • SklearnModel.fit_on_batch()
      • SklearnModel.get_num_tasks()
      • SklearnModel.get_task_type()
      • SklearnModel.load()
      • SklearnModel.model_type
      • SklearnModel.predict()
      • SklearnModel.predict_on_batch()
      • SklearnModel.predict_proba()
      • SklearnModel.save()
  • Module contents
• deepmol.parallelism package
  • Submodules
  • deepmol.parallelism.multiprocessing module
    • JoblibMultiprocessing
      • JoblibMultiprocessing.run()
    • MultiprocessingClass
      • MultiprocessingClass.process
      • MultiprocessingClass.run()
      • MultiprocessingClass.run_iteratively()
    • tqdm_joblib()
  • Module contents
• deepmol.parameter_optimization package
  • Submodules
  • deepmol.parameter_optimization.base_hyperparameter_optimization module
    • HyperparameterOptimizer
      • HyperparameterOptimizer.fit()
  • deepmol.parameter_optimization.deepchem_hyperparameter_optimization module
    • DeepchemBaseSearchCV
      • DeepchemBaseSearchCV.fit()
    • DeepchemGridSearchCV
    • DeepchemRandomSearchCV
  • deepmol.parameter_optimization.hyperparameter_optimization module
    • HyperparameterOptimizerCV
      • HyperparameterOptimizerCV.fit()
    • HyperparameterOptimizerValidation
      • HyperparameterOptimizerValidation.fit()
  • Module contents
• deepmol.pipeline package
  • Submodules
  • deepmol.pipeline.ensemble module
    • VotingPipeline
      • VotingPipeline.evaluate()
      • VotingPipeline.fit()
      • VotingPipeline.is_fitted()
      • VotingPipeline.load()
      • VotingPipeline.predict()
      • VotingPipeline.predict_proba()
      • VotingPipeline.save()
  • deepmol.pipeline.pipeline module
    • Pipeline
      • Pipeline.evaluate()
      • Pipeline.fit()
      • Pipeline.is_fitted()
      • Pipeline.is_prediction_pipeline()
      • Pipeline.load()
      • Pipeline.predict()
      • Pipeline.predict_proba()
      • Pipeline.save()
  • Module contents
• deepmol.pipeline_optimization package
  • Submodules
  • deepmol.pipeline_optimization.objective_wrapper module
  • deepmol.pipeline_optimization.pipeline_optimization module
  • Module contents
• deepmol.scalers package
  • Submodules
  • deepmol.scalers.base_scaler module
    • BaseScaler
      • BaseScaler.load()
      • BaseScaler.save()
      • BaseScaler.scale()
      • BaseScaler.scaler_object
  • deepmol.scalers.sklearn_scalers module
    • Binarizer
    • KernelCenterer
    • MaxAbsScaler
    • MinMaxScaler
    • Normalizer
    • PolynomialFeatures
    • PowerTransformer
    • QuantileTransformer
    • RobustScaler
    • StandardScaler
  • Module contents
• deepmol.splitters package
  • Submodules
  • deepmol.splitters.multitask_splitter module
    • MultiTaskStratifiedSplitter
      • MultiTaskStratifiedSplitter.k_fold_split()
      • MultiTaskStratifiedSplitter.split()
  • deepmol.splitters.splitters module
    • ButinaSplitter
      • ButinaSplitter.k_fold_split()
      • ButinaSplitter.split()
    • RandomSplitter
      • RandomSplitter.k_fold_split()
      • RandomSplitter.split()
    • ScaffoldSplitter
      • ScaffoldSplitter.generate_scaffolds()
      • ScaffoldSplitter.k_fold_split()
      • ScaffoldSplitter.split()
    • SimilaritySplitter
      • SimilaritySplitter.k_fold_split()
      • SimilaritySplitter.split()
    • SingletaskStratifiedSplitter
      • SingletaskStratifiedSplitter.k_fold_split()
      • SingletaskStratifiedSplitter.split()
    • Splitter
      • Splitter.k_fold_split()
      • Splitter.split()
      • Splitter.train_test_split()
      • Splitter.train_valid_test_split()
  • Module contents
• deepmol.standardizer package
  • Submodules
  • deepmol.standardizer.basic_standardizer module
    • BasicStandardizer
  • deepmol.standardizer.chembl_standardizer module
    • ChEMBLStandardizer
  • deepmol.standardizer.custom_standardizer module
    • CustomStandardizer
  • deepmol.standardizer.molecular_standardizer module
    • MolecularStandardizer
      • MolecularStandardizer.standardize()
  • Module contents
• deepmol.tokenizers package
  • Submodules
  • deepmol.tokenizers.atom_level_smiles_tokenizer module
    • AtomLevelSmilesTokenizer
      • AtomLevelSmilesTokenizer.max_length
      • AtomLevelSmilesTokenizer.regex
      • AtomLevelSmilesTokenizer.vocabulary
  • deepmol.tokenizers.kmer_smiles_tokenizer module
    • KmerSmilesTokenizer
      • KmerSmilesTokenizer.atom_level_tokenizer
      • KmerSmilesTokenizer.max_length
      • KmerSmilesTokenizer.regex
      • KmerSmilesTokenizer.size
      • KmerSmilesTokenizer.stride
      • KmerSmilesTokenizer.vocabulary
  • deepmol.tokenizers.tokenizer module
    • Tokenizer
      • Tokenizer.max_length
      • Tokenizer.tokenize()
      • Tokenizer.vocabulary
  • Module contents
• deepmol.unsupervised package
  • Submodules
  • deepmol.unsupervised.base_unsupervised module
    • KMeans
      • KMeans.plot()
    • PCA
      • PCA.plot()
      • PCA.plot_explained_variance()
    • TSNE
      • TSNE.plot()
    • UnsupervisedLearn
      • UnsupervisedLearn.plot()
      • UnsupervisedLearn.run()
  • deepmol.unsupervised.umap module
    • UMAP
      • UMAP.plot()
  • Module contents
• deepmol.utils package
  • Submodules
  • deepmol.utils.cached_properties module
    • deepmol_cached_property
  • deepmol.utils.decorators module
    • inplace_decorator()
    • modify_object_inplace_decorator()
    • timeout()
  • deepmol.utils.errors module
    • PreConditionViolationException
  • deepmol.utils.utils module
    • canonicalize_mol_object()
    • get_class()
    • load_from_disk()
    • load_pickle_file()
    • mol_to_smiles()
    • normalize_labels_shape()
    • smiles_to_mol()
  • Module contents

Module contents