deepmol package

Subpackages

• deepmol.compound_featurization package
  • Submodules
  • deepmol.compound_featurization.base_featurizer module
    • MolecularFeaturizer
      • MolecularFeaturizer.featurize()
  • deepmol.compound_featurization.deepchem_featurizers module
    • ConvMolFeat
    • CoulombEigFeat
    • CoulombFeat
    • MolGanFeat
    • MolGraphConvFeat
    • SmileImageFeat
    • SmilesSeqFeat
      • SmilesSeqFeat.featurize()
    • WeaveFeat
  • deepmol.compound_featurization.mixed_descriptors module
    • MixedFeaturizer
  • deepmol.compound_featurization.mol2vec module
    • Mol2Vec
    • sentences2vec()
  • 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_conformers()
      • 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()
    • handler()
  • deepmol.compound_featurization.rdkit_fingerprints module
    • AtomPairFingerprint
    • AtomPairFingerprintCallbackHash
      • AtomPairFingerprintCallbackHash.hash_function()
    • LayeredFingerprint
    • MACCSkeysFingerprint
    • MorganFingerprint
    • RDKFingerprint
  • Module contents
• deepmol.datasets package
  • Submodules
  • deepmol.datasets.datasets module
    • Dataset
      • Dataset.X
      • 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.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.save_features()
      • SmilesDataset.select()
      • SmilesDataset.select_features_by_index()
      • SmilesDataset.select_features_by_name()
      • SmilesDataset.select_to_split()
      • SmilesDataset.smiles
      • SmilesDataset.to_csv()
      • SmilesDataset.y
  • 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.computeExactShap()
      • ShapValues.computePermutationShap()
      • ShapValues.plotFeatureExplanation()
      • ShapValues.plotHeatMap()
      • ShapValues.plotSampleExplanation()
  • 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.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_models module
    • DeepChemModel
      • DeepChemModel.cross_validate()
      • DeepChemModel.evaluate()
      • DeepChemModel.fit()
      • DeepChemModel.fit_on_batch()
      • DeepChemModel.get_num_tasks()
      • DeepChemModel.get_task_type()
      • DeepChemModel.predict()
      • DeepChemModel.predict_on_batch()
      • DeepChemModel.reload()
      • DeepChemModel.save()
    • generate_sequences()
  • deepmol.models.ensembles module
    • Ensemble
      • Ensemble.evaluate()
      • Ensemble.fit()
      • Ensemble.predict()
    • VotingClassifier
      • VotingClassifier.predict()
  • deepmol.models.keras_models module
    • KerasModel
      • KerasModel.cross_validate()
      • KerasModel.fit()
      • KerasModel.fit_on_batch()
      • KerasModel.get_num_tasks()
      • KerasModel.get_task_type()
      • KerasModel.predict()
      • KerasModel.predict_on_batch()
      • KerasModel.reload()
      • KerasModel.save()
  • deepmol.models.models module
    • Model
      • Model.evaluate()
      • Model.fit()
      • Model.fit_on_batch()
      • Model.get_model_filename()
      • Model.get_num_tasks()
      • Model.get_params_filename()
      • Model.get_task_type()
      • Model.predict()
      • Model.predict_on_batch()
      • Model.predict_proba()
      • Model.reload()
      • Model.save()
  • deepmol.models.sklearn_models module
    • SklearnModel
      • SklearnModel.cross_validate()
      • SklearnModel.fit()
      • SklearnModel.fit_on_batch()
      • SklearnModel.get_num_tasks()
      • SklearnModel.get_task_type()
      • SklearnModel.predict()
      • SklearnModel.predict_on_batch()
      • SklearnModel.reload()
      • SklearnModel.save()
  • Module contents
• deepmol.parallelism package
  • Submodules
  • deepmol.parallelism.multiprocessing module
    • JoblibMultiprocessing
      • JoblibMultiprocessing.run()
    • MultiprocessingClass
      • MultiprocessingClass.process
      • MultiprocessingClass.run()
      • MultiprocessingClass.run_iteratively()
  • Module contents
• deepmol.parameter_optimization package
  • Submodules
  • deepmol.parameter_optimization.deepchem_hyperparameter_optimization module
    • DeepchemBaseSearchCV
      • DeepchemBaseSearchCV.fit()
    • DeepchemGridSearchCV
    • DeepchemRandomSearchCV
  • deepmol.parameter_optimization.hyperparameter_optimization module
    • HyperparameterOptimizer
      • HyperparameterOptimizer.hyperparameter_search()
    • HyperparameterOptimizerCV
      • HyperparameterOptimizerCV.hyperparameter_search()
    • HyperparameterOptimizerValidation
      • HyperparameterOptimizerValidation.hyperparameter_search()
  • Module contents
• deepmol.scalers package
  • Submodules
  • deepmol.scalers.base_scaler module
    • BaseScaler
      • BaseScaler.fit()
      • BaseScaler.fit_transform()
      • BaseScaler.load()
      • BaseScaler.partial_fit()
      • BaseScaler.save()
      • BaseScaler.scaler_object
      • BaseScaler.transform()
  • deepmol.scalers.sklearn_scalers module
    • Binarizer
      • Binarizer.load()
      • Binarizer.partial_fit()
      • Binarizer.scaler_object
    • KernelCenterer
      • KernelCenterer.load()
      • KernelCenterer.partial_fit()
      • KernelCenterer.scaler_object
    • MaxAbsScaler
      • MaxAbsScaler.load()
      • MaxAbsScaler.partial_fit()
      • MaxAbsScaler.scaler_object
    • MinMaxScaler
      • MinMaxScaler.load()
      • MinMaxScaler.partial_fit()
      • MinMaxScaler.scaler_object
    • Normalizer
      • Normalizer.load()
      • Normalizer.partial_fit()
      • Normalizer.scaler_object
    • PolynomialFeatures
      • PolynomialFeatures.load()
      • PolynomialFeatures.partial_fit()
      • PolynomialFeatures.scaler_object
    • PowerTransformer
      • PowerTransformer.load()
      • PowerTransformer.partial_fit()
      • PowerTransformer.scaler_object
    • QuantileTransformer
      • QuantileTransformer.load()
      • QuantileTransformer.partial_fit()
      • QuantileTransformer.scaler_object
    • RobustScaler
      • RobustScaler.load()
      • RobustScaler.partial_fit()
      • RobustScaler.scaler_object
    • StandardScaler
      • StandardScaler.load()
      • StandardScaler.partial_fit()
      • StandardScaler.scaler_object
  • Module contents
• deepmol.splitters package
  • Submodules
  • 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.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_unsupervised()
  • deepmol.unsupervised.umap module
    • UMAP
      • UMAP.plot()
  • Module contents
• deepmol.utils package
  • Submodules
  • deepmol.utils.errors module
    • PreConditionViolationException
  • deepmol.utils.utils module
    • canonicalize_mol_object()
    • draw_MACCS_Pattern()
    • draw_morgan_bit_on_molecule()
    • draw_morgan_bits()
    • draw_rdk_bit_on_molecule()
    • draw_rdk_bits()
    • getSubstructDepiction()
    • load_from_disk()
    • load_pickle_file()
    • mol_to_smiles()
    • moltosvg()
    • normalize_labels_shape()
    • prepareMol()
    • smiles_to_mol()
  • Module contents

Module contents