olorenchemengine

• olorenchemengine package
  • Subpackages
    • olorenchemengine.beta package
      • Submodules
      • olorenchemengine.beta.gnn module
      • olorenchemengine.beta.representations module
      • Module contents
    • olorenchemengine.external package
      • Subpackages
      • Submodules
      • olorenchemengine.external.piCalculax module
      • olorenchemengine.external.stoned module
      • Module contents
    • olorenchemengine.pyg namespace
      • Submodules
      • olorenchemengine.pyg.gcn module
      • olorenchemengine.pyg.util module
    • olorenchemengine.visualizations package
      • Submodules
      • olorenchemengine.visualizations.attribute_section module
      • olorenchemengine.visualizations.compounds module
      • olorenchemengine.visualizations.exploratory_analysis module
      • olorenchemengine.visualizations.matched_pairs module
      • olorenchemengine.visualizations.model_comparisons module
      • olorenchemengine.visualizations.visualization module
      • olorenchemengine.visualizations.visualize_interpret module
      • Module contents
  • Submodules
  • olorenchemengine.base_class module
    • BaseErrorModel
      • BaseErrorModel.build()
      • BaseErrorModel._build()
      • BaseErrorModel.fit()
      • BaseErrorModel.fit_cv()
      • BaseErrorModel._fit()
      • BaseErrorModel.calculate()
      • BaseErrorModel.score()
      • BaseErrorModel.build()
      • BaseErrorModel.calculate()
      • BaseErrorModel.copy()
      • BaseErrorModel.fit()
      • BaseErrorModel.fit_cv()
      • BaseErrorModel.score()
    • BaseModel
      • BaseModel.setting
      • BaseModel.model_name
      • BaseModel.preprocess()
      • BaseModel._fit()
      • BaseModel.fit()
      • BaseModel._predict()
      • BaseModel.predict()
      • BaseModel.test()
      • BaseModel.copy()
      • BaseModel.calibrate()
      • BaseModel.copy()
      • BaseModel.create_error_model()
      • BaseModel.fit()
      • BaseModel.fit_class()
      • BaseModel.fit_cv()
      • BaseModel.predict()
      • BaseModel.preprocess()
      • BaseModel.test()
      • BaseModel.upload_oas()
      • BaseModel.visualize_parameters_ipynb()
    • BaseReduction
      • BaseReduction.fit()
      • BaseReduction.fit_transform()
      • BaseReduction.transform()
      • BaseReduction.fit()
      • BaseReduction.fit_transform()
      • BaseReduction.transform()
    • BaseSKLearnModel
      • BaseSKLearnModel.representation
      • BaseSKLearnModel.regression_model
      • BaseSKLearnModel.classification_model
      • BaseSKLearnModel.preprocess()
    • BaseSKLearnReduction
      • BaseSKLearnReduction.fit()
      • BaseSKLearnReduction.fit_transform()
      • BaseSKLearnReduction.transform()
    • MakeMultiClassModel
      • MakeMultiClassModel.fit()
      • MakeMultiClassModel.predict()
  • olorenchemengine.basics module
    • AutoRandomForestModel
      • AutoRandomForestModel.autofit()
    • BaseMLPClassifier
    • BaseMLPRegressor
    • FeaturesClassification
      • FeaturesClassification.obj
    • GuessingRegression
      • GuessingRegression.transformations
      • GuessingRegression.state
      • GuessingRegression.reg
      • GuessingRegression.linearize()
      • GuessingRegression.preprocess()
    • KBestLinearRegression
    • KNN
    • KNeighborsClassifier
      • KNeighborsClassifier.predict()
    • KNeighborsRegressor
    • LogisticRegression
    • MLP
      • MLP.preprocess()
    • RandomForestClassifier
      • RandomForestClassifier.predict()
    • RandomForestModel
    • RandomForestRegressor
    • RandomizedSearchCVModel
      • RandomizedSearchCVModel.fit()
      • RandomizedSearchCVModel.predict()
    • SVC
    • SVR
    • SklearnMLP
    • SupportVectorMachine
    • TorchMLP
      • TorchMLP.preprocess()
    • XGBClassifier
    • XGBRegressor
    • XGBoostModel
    • ZWK_XGBoostModel
      • ZWK_XGBoostModel.autofit()
  • olorenchemengine.dataset module
    • BaseDataset
      • BaseDataset.entire_dataset
      • BaseDataset.entire_dataset_split
      • BaseDataset.size
      • BaseDataset.test_dataset
      • BaseDataset.train_dataset
      • BaseDataset.trainval_dataset
      • BaseDataset.transform()
      • BaseDataset.valid_dataset
    • BaseDatasetTransform
      • BaseDatasetTransform.transform()
    • BaseKFold
      • BaseKFold.get_n_splits()
      • BaseKFold.transform()
    • CleanStructures
      • CleanStructures.transform()
    • DatasetFromCDDSearch
      • DatasetFromCDDSearch.check_export_status()
      • DatasetFromCDDSearch.get_dataset_cdd_saved_search()
      • DatasetFromCDDSearch.get_export()
      • DatasetFromCDDSearch.run_saved_search()
    • DatasetFromCSV
    • Discretize
      • Discretize.transform()
    • KMeansKFold
      • KMeansKFold.transform()
    • OneHotEncode
      • OneHotEncode.transform()
    • RandomKFold
      • RandomKFold.transform()
    • ScaffoldKFold
      • ScaffoldKFold.transform()
    • ScaffoldKMeansKFold
      • ScaffoldKMeansKFold.transform()
    • func()
  • olorenchemengine.ensemble module
    • Averager
      • Averager.preprocess()
    • BaseBoosting
    • BaseStacking
      • BaseStacking.featurize()
      • BaseStacking.preprocess()
    • BestStacker
    • LinearRegressionStacker
    • MLPStacker
    • RFStacker
    • Resample1
      • Resample1.fit()
    • Resample2
      • Resample2.fit()
    • ResampleAdaboost
    • SKLearnStacker
      • SKLearnStacker.reg_stack
      • SKLearnStacker.class_stack
    • get_oof()
  • olorenchemengine.gnn module
    • AttentiveFP
      • AttentiveFP.create()
      • AttentiveFP.forward()
    • BaseLightningModule
      • BaseLightningModule.configure_optimizers()
      • BaseLightningModule.forward()
      • BaseLightningModule.loss()
      • BaseLightningModule.set_task_type()
      • BaseLightningModule.test_step()
      • BaseLightningModule.training_step()
      • BaseLightningModule.validation_step()
    • BaseTorchGeometricModel
      • BaseTorchGeometricModel.preprocess()
    • TLFromCheckpoint
  • olorenchemengine.hyperparameters module
    • Opt
      • Opt.get_hp
    • OptChoice
      • OptChoice.get_hp
    • OptLogNormal
      • OptLogNormal.get_hp
    • OptLogUniform
      • OptLogUniform.get_hp
    • OptQLogNormal
      • OptQLogNormal.get_hp
    • OptQLogUniform
      • OptQLogUniform.get_hp
    • OptQNormal
      • OptQNormal.get_hp
    • OptQUniform
      • OptQUniform.get_hp
    • OptRandInt
      • OptRandInt.get_hp
    • OptUniform
      • OptUniform.get_hp
    • cast_int()
    • index_hyperparameters()
    • load_hyperparameters()
    • load_hyperparameters_()
    • optimize()
  • olorenchemengine.internal module
    • BaseClass
      • BaseClass.Registry()
      • BaseClass._save()
      • BaseClass._load()
      • BaseClass.AllInstances()
      • BaseClass.Opt()
      • BaseClass.Registry()
      • BaseClass.copy()
    • BaseDepreceated
    • BaseEstimator
      • BaseEstimator.fit()
      • BaseEstimator.predict()
    • BaseObject
      • BaseObject.obj
    • BasePreprocessor
      • BasePreprocessor.fit()
      • BasePreprocessor.fit_transform()
      • BasePreprocessor.transform()
      • BasePreprocessor.inverse_transform()
      • BasePreprocessor.fit()
      • BasePreprocessor.fit_transform()
      • BasePreprocessor.inverse_transform()
      • BasePreprocessor.transform()
    • BaseRemoteSymbol
      • BaseRemoteSymbol.from_rid()
    • BaseRepresentation
      • BaseRepresentation.convert()
    • BaseVecRepresentation
      • BaseVecRepresentation.calculate_distance()
      • BaseVecRepresentation.convert()
      • BaseVecRepresentation.names
    • ConcatenatedVecRepresentation
      • ConcatenatedVecRepresentation.convert()
    • LinearRegression
    • LogScaler
      • LogScaler.fit()
      • LogScaler.fit_transform()
      • LogScaler.inverse_transform()
      • LogScaler.transform()
    • OASConnector
      • OASConnector.authenticate()
      • OASConnector.upload_model()
      • OASConnector.upload_vis()
    • QuantileTransformer
      • QuantileTransformer.obj
    • Remote
    • RemoteObj
    • SMILESRepresentation
      • SMILESRepresentation.convert()
    • StandardScaler
      • StandardScaler.obj
    • all_subclasses()
    • create_BC()
    • deparametrize_args_kwargs()
    • detect_setting()
    • download_public_file()
    • generate_uuid()
    • get_all_reps()
    • get_default_args()
    • get_runtime()
    • import_or_install()
    • install_with_permission()
    • json_params_str()
    • load()
    • loads()
    • log_arguments()
    • mock_imports()
    • model_name_from_model()
    • model_name_from_params()
    • package_available()
    • parameterize()
    • parametrize_args_kwargs()
    • pretty_args_kwargs()
    • pretty_params()
    • pretty_params_str()
    • recursive_get_attr()
    • save()
    • saves()
    • set_runner()
  • olorenchemengine.interpret module
    • CounterfactualEngine
      • CounterfactualEngine.generate_cfs()
      • CounterfactualEngine.generate_samples()
      • CounterfactualEngine.get_cfs()
      • CounterfactualEngine.get_samples()
    • PerturbationEngine
      • PerturbationEngine.get_compound_at_idx()
      • PerturbationEngine.get_compound()
      • PerturbationEngine.get_compound_list()
      • PerturbationEngine.get_compound()
      • PerturbationEngine.get_compound_at_idx()
      • PerturbationEngine.get_compound_list()
    • STONEDMutations
      • STONEDMutations.get_compound_at_idx()
      • STONEDMutations.get_compound()
      • STONEDMutations.get_compound_list()
      • STONEDMutations.get_compound()
      • STONEDMutations.get_compound_at_idx()
      • STONEDMutations.get_compound_list()
    • SwapMutations
      • SwapMutations.get_compound()
      • SwapMutations.get_compound_list()
      • SwapMutations.get_compound()
      • SwapMutations.get_compound_at_idx()
      • SwapMutations.get_compound_list()
      • SwapMutations.get_entry()
      • SwapMutations.get_substitution()
      • SwapMutations.stitch()
    • model_molecule_sensitivity()
  • olorenchemengine.manager module
    • BaseModelManager
      • BaseModelManager.direction
      • BaseModelManager.get_dataset()
      • BaseModelManager.get_model_database()
      • BaseModelManager.primary_metric()
      • BaseModelManager.run()
    • FirebaseModelManager
      • FirebaseModelManager.run()
    • ModelManager
    • SheetsModelManager
    • TOP_MODELS_ADMET()
  • olorenchemengine.reduction module
    • FactorAnalysis
    • PCA
  • olorenchemengine.representations module
    • AtomFeaturizer
      • AtomFeaturizer.length()
      • AtomFeaturizer.convert()
      • AtomFeaturizer.length
    • BaseCompoundVecRepresentation
      • BaseCompoundVecRepresentation.convert()
      • BaseCompoundVecRepresentation.inverse()
    • BondFeaturizer
      • BondFeaturizer.length()
      • BondFeaturizer.convert()
      • BondFeaturizer.length
    • ConcatenatedAtomFeaturizers
      • ConcatenatedAtomFeaturizers.length()
      • ConcatenatedAtomFeaturizers.convert()
      • ConcatenatedAtomFeaturizers.length
    • ConcatenatedBondFeaturizers
      • ConcatenatedBondFeaturizers.length()
      • ConcatenatedBondFeaturizers.convert()
      • ConcatenatedBondFeaturizers.length
    • ConcatenatedStructVecRepresentation
    • DatasetFeatures
      • DatasetFeatures.convert()
    • DescriptastorusDescriptor
      • DescriptastorusDescriptor.AllInstances()
      • DescriptastorusDescriptor.available_descriptors
    • FragmentIndicator
    • GobbiPharma2D
    • GobbiPharma3D
    • LipinskiDescriptor
    • MACCSKeys
    • MCSClusterRep
    • ModelAsRep
    • MordredDescriptor
      • MordredDescriptor.convert()
      • MordredDescriptor.convert_full()
    • MorganVecRepresentation
      • MorganVecRepresentation.info()
    • NoisyVec
    • OGBAtomFeaturizer
      • OGBAtomFeaturizer.convert()
      • OGBAtomFeaturizer.length
    • OGBBondFeaturizer
      • OGBBondFeaturizer.convert()
      • OGBBondFeaturizer.length
    • OlorenCheckpoint
      • OlorenCheckpoint.AllInstances()
      • OlorenCheckpoint.molecule2graph()
      • OlorenCheckpoint.smiles2pyg()
    • PeptideDescriptors1
    • PubChemFingerprint
    • PubChemFingerprint_local
    • TorchGeometricGraph
      • TorchGeometricGraph.dimensions
      • TorchGeometricGraph.convert()
      • TorchGeometricGraph.dimensions
    • countAnyRing()
    • countAromaticRing()
    • countHeteroAromaticRing()
    • countHeteroInRing()
    • countNitrogenInRing()
    • countSaturatedOrAromaticCarbonOnlyRing()
    • countSaturatedOrAromaticHeteroContainingRing()
    • countSaturatedOrAromaticNitrogenContainingRing()
    • countUnsaturatedCarbonOnlyRing()
    • countUnsaturatedHeteroContainingRing()
    • countUnsaturatedNitrogenContainingRing()
    • get_valid_combinations()
    • isAromaticRing()
    • isCarbonOnlyRing()
    • isRingSaturated()
    • isRingUnsaturated()
  • olorenchemengine.splitters module
    • BaseSplitter
      • BaseSplitter.split()
      • BaseSplitter.transform()
    • DateSplitter
      • DateSplitter.split()
      • DateSplitter.split()
    • PropertySplit
      • PropertySplit.split()
    • RandomSplit
      • RandomSplit.split()
      • RandomSplit.split()
    • ScaffoldSplit
      • ScaffoldSplit.split()
      • ScaffoldSplit.split()
    • StratifiedSplitter
      • StratifiedSplitter.split()
      • StratifiedSplitter.split()
    • dc_ScaffoldSplit
      • dc_ScaffoldSplit.split()
      • dc_ScaffoldSplit.split()
    • gg_ScaffoldSplit
      • gg_ScaffoldSplit.split()
      • gg_ScaffoldSplit.generate_scaffold()
      • gg_ScaffoldSplit.gg_split()
      • gg_ScaffoldSplit.split()
  • olorenchemengine.uncertainty module
    • ADAN
      • ADAN.DModX()
      • ADAN.SDEP()
      • ADAN.calculate()
      • ADAN.calculate_full()
      • ADAN.preprocess()
    • AggregateErrorModel
      • AggregateErrorModel.calculate()
      • AggregateErrorModel.fit()
      • AggregateErrorModel.fit_cv()
    • BaseEnsembleModel
      • BaseEnsembleModel.calculate()
    • BaseFingerprintModel
      • BaseFingerprintModel.get_fps()
    • BaseKernelError
    • BootstrapEnsemble
    • KNNSimilarity
    • KernelDistanceError
      • KernelDistanceError.calculate()
    • KernelRegressionError
      • KernelRegressionError.calculate()
    • Naive
      • Naive.calculate()
      • Naive.score()
    • Predicted
      • Predicted.calculate()
    • RandomForestEnsemble
    • SDC
    • TargetDistDC
    • TrainDistDC
  • Module contents
    • BACEDataset()
    • ExampleDataFrame()
    • ExampleDataset()
    • MISSING_DEPENDENCIES()
    • create_config_default_param()
    • online()
    • remove_config_param()
    • set_config_param()
    • test_oce()
    • update_config()