Index

_

_build() (olorenchemengine.base_class.BaseErrorModel method) _fit() (olorenchemengine.base_class.BaseErrorModel method) (olorenchemengine.base_class.BaseModel method)

_load() (olorenchemengine.internal.BaseClass method) _predict() (olorenchemengine.base_class.BaseModel method) _save() (olorenchemengine.internal.BaseClass method)

A

ADAN (class in olorenchemengine.uncertainty) aggregate_at_nodes() (in module olorenchemengine.external.ChemProp.main) AggregateErrorModel (class in olorenchemengine.uncertainty) all_subclasses() (in module olorenchemengine.internal) AllInstances() (olorenchemengine.external.SPGNN.main.SPGNN class method) (olorenchemengine.internal.BaseClass class method) (olorenchemengine.representations.DescriptastorusDescriptor class method) (olorenchemengine.representations.OlorenCheckpoint class method) AtomFeaturizer (class in olorenchemengine.representations) AttentiveFP (class in olorenchemengine.gnn) attribute_name (olorenchemengine.visualizations.attribute_section.ColorPicker attribute) (olorenchemengine.visualizations.attribute_section.DatasetSelector attribute) (olorenchemengine.visualizations.attribute_section.InputNumber attribute) (olorenchemengine.visualizations.attribute_section.InputString attribute) (olorenchemengine.visualizations.attribute_section.ModelSelector attribute)

AttributeSection (class in olorenchemengine.visualizations.attribute_section) authenticate() (olorenchemengine.internal.OASConnector method) autofit() (olorenchemengine.basics.AutoRandomForestModel method) (olorenchemengine.basics.ZWK_XGBoostModel method) AutoRandomForestModel (class in olorenchemengine.basics) available_descriptors (olorenchemengine.representations.DescriptastorusDescriptor attribute) available_pretrained_models (olorenchemengine.external.SPGNN.main.SPGNN attribute), [1] (olorenchemengine.external.SPGNN.main.SPGNNVecRep attribute), [1] Averager (class in olorenchemengine.ensemble)

B

BACEDataset() (in module olorenchemengine) BaseAttribute (class in olorenchemengine.visualizations.attribute_section) BaseBoosting (class in olorenchemengine.ensemble) BaseClass (class in olorenchemengine.internal) BaseCompoundVecRepresentation (class in olorenchemengine.representations) BaseDataset (class in olorenchemengine.dataset) BaseDatasetTransform (class in olorenchemengine.dataset) BaseDepreceated (class in olorenchemengine.internal) BaseEnsembleModel (class in olorenchemengine.uncertainty) BaseErrorModel (class in olorenchemengine.base_class) BaseErrorWaterfall (class in olorenchemengine.visualizations.visualization) BaseEstimator (class in olorenchemengine.internal) BaseFingerprintModel (class in olorenchemengine.uncertainty) BaseKernelError (class in olorenchemengine.uncertainty) BaseKFold (class in olorenchemengine.dataset) BaseLightningModule (class in olorenchemengine.gnn) BaseMLPClassifier (class in olorenchemengine.basics) BaseMLPRegressor (class in olorenchemengine.basics) BaseModel (class in olorenchemengine.base_class)

BaseModelManager (class in olorenchemengine.manager) BaseObject (class in olorenchemengine.internal) BasePreprocessor (class in olorenchemengine.internal) BaseReduction (class in olorenchemengine.base_class) BaseRemoteSymbol (class in olorenchemengine.internal) BaseRepresentation (class in olorenchemengine.internal) BaseSKLearnModel (class in olorenchemengine.base_class) BaseSKLearnReduction (class in olorenchemengine.base_class) BaseSplitter (class in olorenchemengine.splitters) BaseStacking (class in olorenchemengine.ensemble) BaseTorchGeometricModel (class in olorenchemengine.gnn) BaseVecRepresentation (class in olorenchemengine.internal) BaseVisualization (class in olorenchemengine.visualizations.visualization) batch_molecule_to_pyg() (in module olorenchemengine.pyg.util) BestStacker (class in olorenchemengine.ensemble) bew() (olorenchemengine.external.GaussianProcess.main.Tanimoto method) BondFeaturizer (class in olorenchemengine.representations) BootstrapEnsemble (class in olorenchemengine.uncertainty) build() (olorenchemengine.base_class.BaseErrorModel method), [1]

C

calc_pI (class in olorenchemengine.external.piCalculax) calculate() (olorenchemengine.base_class.BaseErrorModel method), [1] (olorenchemengine.uncertainty.ADAN method) (olorenchemengine.uncertainty.AggregateErrorModel method) (olorenchemengine.uncertainty.BaseEnsembleModel method) (olorenchemengine.uncertainty.KernelDistanceError method) (olorenchemengine.uncertainty.KernelRegressionError method) (olorenchemengine.uncertainty.Naive method) (olorenchemengine.uncertainty.Predicted method) calculate_distance() (olorenchemengine.internal.BaseVecRepresentation method) calculate_full() (olorenchemengine.uncertainty.ADAN method) calibrate() (olorenchemengine.base_class.BaseModel method) cast_int() (in module olorenchemengine.hyperparameters) charge() (in module olorenchemengine.external.piCalculax) check_export_status() (olorenchemengine.dataset.DatasetFromCDDSearch method) ChemicalSpacePlot (class in olorenchemengine.visualizations.visualization) ChemProp_AF (class in olorenchemengine.external.ChemProp.main) ChemProp_BF (class in olorenchemengine.external.ChemProp.main) ChemPropDataLoading (class in olorenchemengine.external.ChemProp.main) ChemPropModel (class in olorenchemengine.external.ChemProp.main) class_stack (olorenchemengine.ensemble.SKLearnStacker attribute) classification_model (olorenchemengine.base_class.BaseSKLearnModel attribute) CleanStructures (class in olorenchemengine.dataset) ColorPicker (class in olorenchemengine.visualizations.attribute_section) CompoundScatterPlot (class in olorenchemengine.visualizations.visualization) ConcatenatedAtomFeaturizers (class in olorenchemengine.representations) ConcatenatedBondFeaturizers (class in olorenchemengine.representations) ConcatenatedStructVecRepresentation (class in olorenchemengine.representations) ConcatenatedVecRepresentation (class in olorenchemengine.internal) configure_optimizers() (olorenchemengine.gnn.BaseLightningModule method) contains() (olorenchemengine.external.mol2vec.operations.MolSentence method) convert() (olorenchemengine.beta.representations.SimLookup_beta method) (olorenchemengine.external.ChemProp.main.ChemProp_AF method) (olorenchemengine.external.ChemProp.main.ChemProp_BF method) (olorenchemengine.external.MolCLR.main.MolCLR_AF method) (olorenchemengine.external.MolCLR.main.MolCLR_BF method) (olorenchemengine.external.MolCLR.main.MolCLRVecRep method) (olorenchemengine.external.SPGNN.main.SPGNN_AF method) (olorenchemengine.external.SPGNN.main.SPGNN_BF method) (olorenchemengine.external.SPGNN.main.SPGNNVecRep method) (olorenchemengine.internal.BaseRepresentation method) (olorenchemengine.internal.BaseVecRepresentation method) (olorenchemengine.internal.ConcatenatedVecRepresentation method) (olorenchemengine.internal.SMILESRepresentation method) (olorenchemengine.representations.AtomFeaturizer method) (olorenchemengine.representations.BaseCompoundVecRepresentation method) (olorenchemengine.representations.BondFeaturizer method) (olorenchemengine.representations.ConcatenatedAtomFeaturizers method) (olorenchemengine.representations.ConcatenatedBondFeaturizers method) (olorenchemengine.representations.DatasetFeatures method) (olorenchemengine.representations.MordredDescriptor method) (olorenchemengine.representations.OGBAtomFeaturizer method) (olorenchemengine.representations.OGBBondFeaturizer method) (olorenchemengine.representations.TorchGeometricGraph method)

convert_full() (olorenchemengine.representations.MordredDescriptor method) copy() (olorenchemengine.base_class.BaseErrorModel method) (olorenchemengine.base_class.BaseModel method), [1] (olorenchemengine.internal.BaseClass method) countAnyRing() (in module olorenchemengine.representations) countAromaticRing() (in module olorenchemengine.representations) CounterfactualEngine (class in olorenchemengine.interpret) countHeteroAromaticRing() (in module olorenchemengine.representations) countHeteroInRing() (in module olorenchemengine.representations) countNitrogenInRing() (in module olorenchemengine.representations) countSaturatedOrAromaticCarbonOnlyRing() (in module olorenchemengine.representations) countSaturatedOrAromaticHeteroContainingRing() (in module olorenchemengine.representations) countSaturatedOrAromaticNitrogenContainingRing() (in module olorenchemengine.representations) countUnsaturatedCarbonOnlyRing() (in module olorenchemengine.representations) countUnsaturatedHeteroContainingRing() (in module olorenchemengine.representations) countUnsaturatedNitrogenContainingRing() (in module olorenchemengine.representations) create() (olorenchemengine.beta.gnn.SuperGATModel_beta method) (olorenchemengine.gnn.AttentiveFP method) create_BC() (in module olorenchemengine.internal) create_config_default_param() (in module olorenchemengine) create_error_model() (olorenchemengine.base_class.BaseModel method) criterion (olorenchemengine.external.ChemProp.main.ChemPropModel attribute)

D

DatasetFeatures (class in olorenchemengine.representations) DatasetFromCDDSearch (class in olorenchemengine.dataset) DatasetFromCSV (class in olorenchemengine.dataset) DatasetSelector (class in olorenchemengine.visualizations.attribute_section) DateSplitter (class in olorenchemengine.splitters) dc_ScaffoldSplit (class in olorenchemengine.splitters) deparametrize_args_kwargs() (in module olorenchemengine.internal) DescriptastorusDescriptor (class in olorenchemengine.representations) detect_setting() (in module olorenchemengine.internal)

DfVec (class in olorenchemengine.external.mol2vec.operations) diag() (olorenchemengine.external.GaussianProcess.main.Tanimoto method) dimensions (olorenchemengine.representations.TorchGeometricGraph attribute) (olorenchemengine.representations.TorchGeometricGraph property) directed_mp() (in module olorenchemengine.external.ChemProp.main) direction (olorenchemengine.manager.BaseModelManager property) Discretize (class in olorenchemengine.dataset) DModX() (olorenchemengine.uncertainty.ADAN method) download_public_file() (in module olorenchemengine.internal)

E

entire_dataset (olorenchemengine.dataset.BaseDataset property) entire_dataset_split (olorenchemengine.dataset.BaseDataset property)

ExampleDataFrame() (in module olorenchemengine) ExampleDataset() (in module olorenchemengine) extend() (olorenchemengine.external.HondaSTRep.operations.TorchVocab method)

F

FactorAnalysis (class in olorenchemengine.reduction) FeaturesClassification (class in olorenchemengine.basics) featurize() (in module olorenchemengine.external.mol2vec.operations) (olorenchemengine.ensemble.BaseStacking method) find_pKas() (in module olorenchemengine.external.piCalculax) FirebaseModelManager (class in olorenchemengine.manager) fit() (olorenchemengine.base_class.BaseErrorModel method), [1] (olorenchemengine.base_class.BaseModel method), [1] (olorenchemengine.base_class.BaseReduction method), [1] (olorenchemengine.base_class.BaseSKLearnReduction method) (olorenchemengine.base_class.MakeMultiClassModel method) (olorenchemengine.basics.RandomizedSearchCVModel method) (olorenchemengine.ensemble.Resample1 method) (olorenchemengine.ensemble.Resample2 method) (olorenchemengine.internal.BaseEstimator method) (olorenchemengine.internal.BasePreprocessor method), [1] (olorenchemengine.internal.LogScaler method) (olorenchemengine.uncertainty.AggregateErrorModel method)

fit_class() (olorenchemengine.base_class.BaseModel method) fit_cv() (olorenchemengine.base_class.BaseErrorModel method), [1] (olorenchemengine.base_class.BaseModel method) (olorenchemengine.uncertainty.AggregateErrorModel method) fit_transform() (olorenchemengine.base_class.BaseReduction method), [1] (olorenchemengine.base_class.BaseSKLearnReduction method) (olorenchemengine.internal.BasePreprocessor method), [1] (olorenchemengine.internal.LogScaler method) forward() (olorenchemengine.beta.gnn.SuperGATModel_beta method) (olorenchemengine.gnn.AttentiveFP method) (olorenchemengine.gnn.BaseLightningModule method) FragmentIndicator (class in olorenchemengine.representations) from_attributes() (olorenchemengine.visualizations.visualization.BaseVisualization class method) (olorenchemengine.visualizations.visualization.VisualizeDatasetDivision class method) from_rid() (olorenchemengine.internal.BaseRemoteSymbol class method) from_seq() (olorenchemengine.external.HondaSTRep.operations.Vocab method) (olorenchemengine.external.HondaSTRep.operations.WordVocab method) func() (in module olorenchemengine.dataset)

G

GaussianProcessClassifier (class in olorenchemengine.external.GaussianProcess.main) GaussianProcessModel (class in olorenchemengine.external.GaussianProcess.main) GaussianProcessRegressor (class in olorenchemengine.external.GaussianProcess.main) generate_cfs() (olorenchemengine.interpret.CounterfactualEngine method) generate_corpus() (in module olorenchemengine.external.mol2vec.operations) generate_samples() (olorenchemengine.interpret.CounterfactualEngine method) generate_scaffold() (olorenchemengine.splitters.gg_ScaffoldSplit method) generate_uuid() (in module olorenchemengine.internal) get_all_reps() (in module olorenchemengine.internal) get_attributes() (olorenchemengine.visualizations.visualization.BaseVisualization static method) (olorenchemengine.visualizations.visualization.CompoundScatterPlot static method) (olorenchemengine.visualizations.visualization.ModelPR static method) (olorenchemengine.visualizations.visualization.ModelROC static method) (olorenchemengine.visualizations.visualization.ModelROCThreshold static method) (olorenchemengine.visualizations.visualization.MorganContributions static method) (olorenchemengine.visualizations.visualization.VisualizeADAN static method) (olorenchemengine.visualizations.visualization.VisualizeDatasetDivision static method) (olorenchemengine.visualizations.visualization.VisualizeModelSim static method) (olorenchemengine.visualizations.visualization.VisualizeModelSim2 static method) get_cfs() (olorenchemengine.interpret.CounterfactualEngine method) get_compound() (olorenchemengine.interpret.PerturbationEngine method), [1] (olorenchemengine.interpret.STONEDMutations method), [1] (olorenchemengine.interpret.SwapMutations method), [1] get_compound_at_idx() (olorenchemengine.interpret.PerturbationEngine method), [1] (olorenchemengine.interpret.STONEDMutations method), [1] (olorenchemengine.interpret.SwapMutations method) get_compound_list() (olorenchemengine.interpret.PerturbationEngine method), [1] (olorenchemengine.interpret.STONEDMutations method), [1] (olorenchemengine.interpret.SwapMutations method), [1] get_data() (olorenchemengine.visualizations.exploratory_analysis.VisualizeFeatures method) (olorenchemengine.visualizations.matched_pairs.MatchedPairsHeatmap method) (olorenchemengine.visualizations.matched_pairs.MatchedPairsTable method) (olorenchemengine.visualizations.model_comparisons.ModelOverTime method) (olorenchemengine.visualizations.model_comparisons.VisualizationModelManager_Bar method) (olorenchemengine.visualizations.visualization.BaseErrorWaterfall method) (olorenchemengine.visualizations.visualization.BaseVisualization method) (olorenchemengine.visualizations.visualization.ChemicalSpacePlot method) (olorenchemengine.visualizations.visualization.CompoundScatterPlot method) (olorenchemengine.visualizations.visualization.ModelPR method) (olorenchemengine.visualizations.visualization.ModelROC method) (olorenchemengine.visualizations.visualization.ModelROCThreshold method) (olorenchemengine.visualizations.visualization.MorganContributions method) (olorenchemengine.visualizations.visualization.ScatterPlot method) (olorenchemengine.visualizations.visualization.VisualizeADAN method) (olorenchemengine.visualizations.visualization.VisualizeCompounds method) (olorenchemengine.visualizations.visualization.VisualizeCounterfactual method) (olorenchemengine.visualizations.visualization.VisualizeDatasetDivision method) (olorenchemengine.visualizations.visualization.VisualizeError method) (olorenchemengine.visualizations.visualization.VisualizeModelSim method) (olorenchemengine.visualizations.visualization.VisualizeModelSim2 method) (olorenchemengine.visualizations.visualize_interpret.VisualizePredictionSensitivity method)

get_dataset() (olorenchemengine.manager.BaseModelManager method) get_dataset_cdd_saved_search() (olorenchemengine.dataset.DatasetFromCDDSearch method) get_default_args() (in module olorenchemengine.internal) get_entry() (olorenchemengine.interpret.SwapMutations method) get_export() (olorenchemengine.dataset.DatasetFromCDDSearch method) get_fps() (olorenchemengine.uncertainty.BaseFingerprintModel method) get_hp (olorenchemengine.hyperparameters.Opt property) (olorenchemengine.hyperparameters.OptChoice property) (olorenchemengine.hyperparameters.OptLogNormal property) (olorenchemengine.hyperparameters.OptLogUniform property) (olorenchemengine.hyperparameters.OptQLogNormal property) (olorenchemengine.hyperparameters.OptQLogUniform property) (olorenchemengine.hyperparameters.OptQNormal property) (olorenchemengine.hyperparameters.OptQUniform property) (olorenchemengine.hyperparameters.OptRandInt property) (olorenchemengine.hyperparameters.OptUniform property) get_html() (olorenchemengine.visualizations.visualization.BaseVisualization method) (olorenchemengine.visualizations.visualization.MorganContributions method) get_js() (olorenchemengine.visualizations.visualization.BaseVisualization method) get_link() (olorenchemengine.visualizations.visualization.BaseVisualization method) get_model_database() (olorenchemengine.manager.BaseModelManager method) get_mutated_SELFIES() (in module olorenchemengine.external.stoned) get_n_splits() (olorenchemengine.dataset.BaseKFold method) get_oas_compatible_visualizations() (in module olorenchemengine.visualizations.visualization) get_oof() (in module olorenchemengine.ensemble) get_runtime() (in module olorenchemengine.internal) get_samples() (olorenchemengine.interpret.CounterfactualEngine method) get_selfie_chars() (in module olorenchemengine.external.stoned) get_substitution() (olorenchemengine.interpret.SwapMutations method) get_substructures() (olorenchemengine.visualizations.visualization.MorganContributions method) get_valid_combinations() (in module olorenchemengine.representations) getSubstructSmi() (olorenchemengine.visualizations.visualization.MorganContributions method) gg_ScaffoldSplit (class in olorenchemengine.splitters) gg_split() (olorenchemengine.splitters.gg_ScaffoldSplit method) GINModel (class in olorenchemengine.external.GINNetwork.main) GobbiPharma2D (class in olorenchemengine.representations) GobbiPharma3D (class in olorenchemengine.representations) GuessingRegression (class in olorenchemengine.basics)

H

HondaSTRep (class in olorenchemengine.external.HondaSTRep.main)

hyperparameter_sigma_0 (olorenchemengine.external.GaussianProcess.main.Tanimoto property)

I

import_or_install() (in module olorenchemengine.internal) index_hyperparameters() (in module olorenchemengine.hyperparameters) info() (olorenchemengine.representations.MorganVecRepresentation method) initialize_weights() (in module olorenchemengine.external.ChemProp.main) InputNumber (class in olorenchemengine.visualizations.attribute_section) InputString (class in olorenchemengine.visualizations.attribute_section) InputThreshold (class in olorenchemengine.visualizations.attribute_section) insert_unk() (in module olorenchemengine.external.mol2vec.operations)

install_with_permission() (in module olorenchemengine.internal) inverse() (olorenchemengine.representations.BaseCompoundVecRepresentation method) inverse_transform() (olorenchemengine.internal.BasePreprocessor method), [1] (olorenchemengine.internal.LogScaler method) is_stationary() (olorenchemengine.external.GaussianProcess.main.Tanimoto method) isAromaticRing() (in module olorenchemengine.representations) isCarbonOnlyRing() (in module olorenchemengine.representations) isRingSaturated() (in module olorenchemengine.representations) isRingUnsaturated() (in module olorenchemengine.representations)

J

JS_NAME (olorenchemengine.visualizations.compounds.VisualizeMCS property) (olorenchemengine.visualizations.matched_pairs.MatchedPairsHeatmap property) (olorenchemengine.visualizations.matched_pairs.MatchedPairsTable property) (olorenchemengine.visualizations.model_comparisons.VisualizationModelManager_Bar property) (olorenchemengine.visualizations.visualization.BaseVisualization property) (olorenchemengine.visualizations.visualization.CompoundScatterPlot property) (olorenchemengine.visualizations.visualization.ModelPR property) (olorenchemengine.visualizations.visualization.ModelROC property) (olorenchemengine.visualizations.visualization.ModelROCThreshold property) (olorenchemengine.visualizations.visualization.MorganContributions property)

json_params_str() (in module olorenchemengine.internal)

K

KBestLinearRegression (class in olorenchemengine.basics) KernelDistanceError (class in olorenchemengine.uncertainty) KernelRegressionError (class in olorenchemengine.uncertainty) KMeansKFold (class in olorenchemengine.dataset)

KNeighborsClassifier (class in olorenchemengine.basics) KNeighborsRegressor (class in olorenchemengine.basics) KNN (class in olorenchemengine.basics) KNNSimilarity (class in olorenchemengine.uncertainty)

L

length (olorenchemengine.external.ChemProp.main.ChemProp_AF property) (olorenchemengine.external.ChemProp.main.ChemProp_BF property) (olorenchemengine.external.MolCLR.main.MolCLR_AF property) (olorenchemengine.external.MolCLR.main.MolCLR_BF property) (olorenchemengine.external.SPGNN.main.SPGNN_AF property) (olorenchemengine.external.SPGNN.main.SPGNN_BF property) (olorenchemengine.representations.AtomFeaturizer property) (olorenchemengine.representations.BondFeaturizer property) (olorenchemengine.representations.ConcatenatedAtomFeaturizers property) (olorenchemengine.representations.ConcatenatedBondFeaturizers property) (olorenchemengine.representations.OGBAtomFeaturizer property) (olorenchemengine.representations.OGBBondFeaturizer property) length() (olorenchemengine.representations.AtomFeaturizer method) (olorenchemengine.representations.BondFeaturizer method) (olorenchemengine.representations.ConcatenatedAtomFeaturizers method) (olorenchemengine.representations.ConcatenatedBondFeaturizers method)

linearize() (olorenchemengine.basics.GuessingRegression method) LinearRegression (class in olorenchemengine.internal) LinearRegressionStacker (class in olorenchemengine.ensemble) LipinskiDescriptor (class in olorenchemengine.representations) load() (in module olorenchemengine.internal) load_hyperparameters() (in module olorenchemengine.hyperparameters) load_hyperparameters_() (in module olorenchemengine.hyperparameters) load_vocab() (olorenchemengine.external.HondaSTRep.operations.Vocab static method) (olorenchemengine.external.HondaSTRep.operations.WordVocab static method) loads() (in module olorenchemengine.internal) log_arguments() (in module olorenchemengine.internal) LogisticRegression (class in olorenchemengine.basics) LogScaler (class in olorenchemengine.internal) loss() (olorenchemengine.gnn.BaseLightningModule method)

M

MACCSKeys (class in olorenchemengine.representations) make_multihop_edges() (in module olorenchemengine.external.GINNetwork.operations) MakeMultiClassModel (class in olorenchemengine.base_class) matched_pairs() (olorenchemengine.visualizations.matched_pairs.MatchedPairsTable method) MatchedPairsHeatmap (class in olorenchemengine.visualizations.matched_pairs) MatchedPairsTable (class in olorenchemengine.visualizations.matched_pairs) MCSClusterRep (class in olorenchemengine.representations) MISSING_DEPENDENCIES() (in module olorenchemengine) MLP (class in olorenchemengine.basics) MLPStacker (class in olorenchemengine.ensemble) mock_imports() (in module olorenchemengine.internal) model_config (olorenchemengine.external.MolCLR.main.MolCLR attribute) (olorenchemengine.external.MolCLR.main.MolCLRVecRep attribute) model_molecule_sensitivity() (in module olorenchemengine.interpret) model_name (olorenchemengine.base_class.BaseModel attribute) model_name_from_model() (in module olorenchemengine.internal) model_name_from_params() (in module olorenchemengine.internal) ModelAsRep (class in olorenchemengine.representations) ModelManager (class in olorenchemengine.manager) ModelOverTime (class in olorenchemengine.visualizations.model_comparisons) ModelPR (class in olorenchemengine.visualizations.visualization) ModelROC (class in olorenchemengine.visualizations.visualization) ModelROCThreshold (class in olorenchemengine.visualizations.visualization) ModelSelector (class in olorenchemengine.visualizations.attribute_section) module olorenchemengine olorenchemengine.base_class olorenchemengine.basics olorenchemengine.beta olorenchemengine.beta.gnn olorenchemengine.beta.representations olorenchemengine.dataset olorenchemengine.ensemble olorenchemengine.external olorenchemengine.external.ChemProp olorenchemengine.external.ChemProp.main olorenchemengine.external.GaussianProcess olorenchemengine.external.GaussianProcess.main olorenchemengine.external.GINNetwork olorenchemengine.external.GINNetwork.main olorenchemengine.external.GINNetwork.operations olorenchemengine.external.HondaSTRep olorenchemengine.external.HondaSTRep.main olorenchemengine.external.HondaSTRep.operations olorenchemengine.external.mol2vec olorenchemengine.external.mol2vec.main olorenchemengine.external.mol2vec.operations olorenchemengine.external.MolCLR olorenchemengine.external.MolCLR.main olorenchemengine.external.piCalculax olorenchemengine.external.SPGNN olorenchemengine.external.SPGNN.main olorenchemengine.external.SPGNN.model olorenchemengine.external.stoned olorenchemengine.gnn olorenchemengine.hyperparameters olorenchemengine.internal olorenchemengine.interpret olorenchemengine.manager olorenchemengine.pyg olorenchemengine.pyg.gcn olorenchemengine.pyg.util olorenchemengine.reduction olorenchemengine.representations olorenchemengine.splitters olorenchemengine.uncertainty olorenchemengine.visualizations olorenchemengine.visualizations.attribute_section olorenchemengine.visualizations.compounds olorenchemengine.visualizations.exploratory_analysis olorenchemengine.visualizations.matched_pairs olorenchemengine.visualizations.model_comparisons olorenchemengine.visualizations.visualization olorenchemengine.visualizations.visualize_interpret

mol2alt_sentence() (in module olorenchemengine.external.mol2vec.operations) mol2sentence() (in module olorenchemengine.external.mol2vec.operations) Mol2Vec (class in olorenchemengine.external.mol2vec.main) MolCLR (class in olorenchemengine.external.MolCLR.main) MolCLR_AF (class in olorenchemengine.external.MolCLR.main) MolCLR_BF (class in olorenchemengine.external.MolCLR.main) MolCLR_PYG (class in olorenchemengine.external.MolCLR.main) MolCLRVecRep (class in olorenchemengine.external.MolCLR.main) molecule2graph() (olorenchemengine.representations.OlorenCheckpoint method) molecule_to_graph() (in module olorenchemengine.pyg.util) molecule_to_pyg() (in module olorenchemengine.pyg.util) MolSentence (class in olorenchemengine.external.mol2vec.operations) MordredDescriptor (class in olorenchemengine.representations) MorganContributions (class in olorenchemengine.visualizations.visualization) MorganVecRepresentation (class in olorenchemengine.representations) mutate_selfie() (in module olorenchemengine.external.stoned)

N

Naive (class in olorenchemengine.uncertainty) names (olorenchemengine.internal.BaseVecRepresentation property)

new() (in module olorenchemengine.external.GINNetwork.operations) NoisyVec (class in olorenchemengine.representations)

O

OASConnector (class in olorenchemengine.internal) obj (olorenchemengine.basics.FeaturesClassification attribute) (olorenchemengine.internal.BaseObject attribute) (olorenchemengine.internal.QuantileTransformer attribute) (olorenchemengine.internal.StandardScaler attribute) OGBAtomFeaturizer (class in olorenchemengine.representations) OGBBondFeaturizer (class in olorenchemengine.representations) OlorenCheckpoint (class in olorenchemengine.representations) olorenchemengine module olorenchemengine.base_class module olorenchemengine.basics module olorenchemengine.beta module olorenchemengine.beta.gnn module olorenchemengine.beta.representations module olorenchemengine.dataset module olorenchemengine.ensemble module olorenchemengine.external module olorenchemengine.external.ChemProp module olorenchemengine.external.ChemProp.main module olorenchemengine.external.GaussianProcess module olorenchemengine.external.GaussianProcess.main module olorenchemengine.external.GINNetwork module olorenchemengine.external.GINNetwork.main module olorenchemengine.external.GINNetwork.operations module olorenchemengine.external.HondaSTRep module olorenchemengine.external.HondaSTRep.main module olorenchemengine.external.HondaSTRep.operations module olorenchemengine.external.mol2vec module olorenchemengine.external.mol2vec.main module olorenchemengine.external.mol2vec.operations module olorenchemengine.external.MolCLR module olorenchemengine.external.MolCLR.main module olorenchemengine.external.piCalculax module olorenchemengine.external.SPGNN module olorenchemengine.external.SPGNN.main module

olorenchemengine.external.SPGNN.model module olorenchemengine.external.stoned module olorenchemengine.gnn module olorenchemengine.hyperparameters module olorenchemengine.internal module olorenchemengine.interpret module olorenchemengine.manager module olorenchemengine.pyg module olorenchemengine.pyg.gcn module olorenchemengine.pyg.util module olorenchemengine.reduction module olorenchemengine.representations module olorenchemengine.splitters module olorenchemengine.uncertainty module olorenchemengine.visualizations module 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 OneHotEncode (class in olorenchemengine.dataset) onek_encoding_unk() (in module olorenchemengine.external.ChemProp.main) online() (in module olorenchemengine) Opt (class in olorenchemengine.hyperparameters) Opt() (olorenchemengine.internal.BaseClass class method) OptChoice (class in olorenchemengine.hyperparameters) optimize() (in module olorenchemengine.hyperparameters) optimizer (olorenchemengine.external.ChemProp.main.ChemPropModel attribute) OptLogNormal (class in olorenchemengine.hyperparameters) OptLogUniform (class in olorenchemengine.hyperparameters) OptQLogNormal (class in olorenchemengine.hyperparameters) OptQLogUniform (class in olorenchemengine.hyperparameters) OptQNormal (class in olorenchemengine.hyperparameters) OptQUniform (class in olorenchemengine.hyperparameters) OptRandInt (class in olorenchemengine.hyperparameters) OptUniform (class in olorenchemengine.hyperparameters)

P

package_available() (in module olorenchemengine.internal) package_urls (olorenchemengine.visualizations.visualization.BaseVisualization attribute) parameterize() (in module olorenchemengine.internal) parametrize_args_kwargs() (in module olorenchemengine.internal) PCA (class in olorenchemengine.reduction) pca_df() (olorenchemengine.visualizations.visualization.ChemicalSpacePlot method) PeptideDescriptors1 (class in olorenchemengine.representations) PerturbationEngine (class in olorenchemengine.interpret) pI() (in module olorenchemengine.external.piCalculax) predict() (in module olorenchemengine.external.ChemProp.main) (in module olorenchemengine.external.SPGNN.main) (olorenchemengine.base_class.BaseModel method), [1] (olorenchemengine.base_class.MakeMultiClassModel method) (olorenchemengine.basics.KNeighborsClassifier method) (olorenchemengine.basics.RandomForestClassifier method) (olorenchemengine.basics.RandomizedSearchCVModel method) (olorenchemengine.internal.BaseEstimator method) Predicted (class in olorenchemengine.uncertainty)

preprocess() (olorenchemengine.base_class.BaseModel method), [1] (olorenchemengine.base_class.BaseSKLearnModel method) (olorenchemengine.basics.GuessingRegression method) (olorenchemengine.basics.MLP method) (olorenchemengine.basics.TorchMLP method) (olorenchemengine.ensemble.Averager method) (olorenchemengine.ensemble.BaseStacking method) (olorenchemengine.external.ChemProp.main.ChemPropModel method) (olorenchemengine.external.MolCLR.main.MolCLR method) (olorenchemengine.external.SPGNN.main.SPGNN method) (olorenchemengine.gnn.BaseTorchGeometricModel method) (olorenchemengine.uncertainty.ADAN method) pretty_args_kwargs() (in module olorenchemengine.internal) pretty_params() (in module olorenchemengine.internal) pretty_params_str() (in module olorenchemengine.internal) primary_metric() (olorenchemengine.manager.BaseModelManager method) PropertySplit (class in olorenchemengine.splitters) PubChemFingerprint (class in olorenchemengine.representations) PubChemFingerprint_local (class in olorenchemengine.representations)

Q

QuantileTransformer (class in olorenchemengine.internal)

R

RandomForestClassifier (class in olorenchemengine.basics) RandomForestEnsemble (class in olorenchemengine.uncertainty) RandomForestModel (class in olorenchemengine.basics) RandomForestRegressor (class in olorenchemengine.basics) randomize_smiles() (in module olorenchemengine.external.stoned) RandomizedSearchCVModel (class in olorenchemengine.basics) RandomKFold (class in olorenchemengine.dataset) RandomSplit (class in olorenchemengine.splitters) recursive_get_attr() (in module olorenchemengine.internal) reg (olorenchemengine.basics.GuessingRegression attribute) reg_stack (olorenchemengine.ensemble.SKLearnStacker attribute) Registry() (olorenchemengine.internal.BaseClass class method) (olorenchemengine.internal.BaseClass method) regression_model (olorenchemengine.base_class.BaseSKLearnModel attribute) Remote (class in olorenchemengine.internal) RemoteObj (class in olorenchemengine.internal)

remove_config_param() (in module olorenchemengine) remove_salts_solvents() (in module olorenchemengine.external.mol2vec.operations) render() (olorenchemengine.visualizations.visualization.BaseVisualization method) render_data_url() (olorenchemengine.visualizations.visualization.BaseVisualization method) render_ipynb() (olorenchemengine.visualizations.model_comparisons.VisualizationModelManager_Bar method) (olorenchemengine.visualizations.visualization.BaseVisualization method) render_oas() (olorenchemengine.visualizations.visualization.BaseVisualization method) representation (olorenchemengine.base_class.BaseSKLearnModel attribute) (olorenchemengine.external.ChemProp.main.ChemPropModel attribute) Resample1 (class in olorenchemengine.ensemble) Resample2 (class in olorenchemengine.ensemble) ResampleAdaboost (class in olorenchemengine.ensemble) RFStacker (class in olorenchemengine.ensemble) run() (olorenchemengine.manager.BaseModelManager method) (olorenchemengine.manager.FirebaseModelManager method) run_saved_search() (olorenchemengine.dataset.DatasetFromCDDSearch method)

S

sanitize_smiles() (in module olorenchemengine.external.stoned) save() (in module olorenchemengine.internal) save_html() (olorenchemengine.visualizations.visualization.BaseVisualization method) save_vocab() (olorenchemengine.external.HondaSTRep.operations.Vocab method) saves() (in module olorenchemengine.internal) ScaffoldKFold (class in olorenchemengine.dataset) ScaffoldKMeansKFold (class in olorenchemengine.dataset) ScaffoldSplit (class in olorenchemengine.splitters) ScatterPlot (class in olorenchemengine.visualizations.visualization) scheduler (olorenchemengine.external.ChemProp.main.ChemPropModel attribute) score() (olorenchemengine.base_class.BaseErrorModel method), [1] (olorenchemengine.uncertainty.Naive method) SDC (class in olorenchemengine.uncertainty) SDEP() (olorenchemengine.uncertainty.ADAN method) sentences2vec() (in module olorenchemengine.external.mol2vec.operations) set_config_param() (in module olorenchemengine) set_runner() (in module olorenchemengine.internal) set_task_type() (olorenchemengine.gnn.BaseLightningModule method) setting (olorenchemengine.base_class.BaseModel attribute) (olorenchemengine.external.ChemProp.main.ChemPropModel attribute) SheetsModelManager (class in olorenchemengine.manager) SimLookup_beta (class in olorenchemengine.beta.representations) SimpleAttribute (class in olorenchemengine.visualizations.attribute_section) size (olorenchemengine.dataset.BaseDataset property) SklearnMLP (class in olorenchemengine.basics) SKLearnStacker (class in olorenchemengine.ensemble)

smiles2pyg() (olorenchemengine.representations.OlorenCheckpoint method) SMILESRepresentation (class in olorenchemengine.internal) SPGNN (class in olorenchemengine.external.SPGNN.main) SPGNN_AF (class in olorenchemengine.external.SPGNN.main) SPGNN_BF (class in olorenchemengine.external.SPGNN.main) SPGNN_PYG (class in olorenchemengine.external.SPGNN.main) SPGNNVecRep (class in olorenchemengine.external.SPGNN.main) split() (in module olorenchemengine.external.HondaSTRep.operations) (olorenchemengine.splitters.BaseSplitter method) (olorenchemengine.splitters.DateSplitter method), [1] (olorenchemengine.splitters.dc_ScaffoldSplit method), [1] (olorenchemengine.splitters.gg_ScaffoldSplit method), [1] (olorenchemengine.splitters.PropertySplit method) (olorenchemengine.splitters.RandomSplit method), [1] (olorenchemengine.splitters.ScaffoldSplit method), [1] (olorenchemengine.splitters.StratifiedSplitter method), [1] StandardScaler (class in olorenchemengine.internal) state (olorenchemengine.basics.GuessingRegression attribute) stitch() (olorenchemengine.interpret.SwapMutations method) STONEDMutations (class in olorenchemengine.interpret) StratifiedSplitter (class in olorenchemengine.splitters) SuperGATModel_beta (class in olorenchemengine.beta.gnn) SupportVectorMachine (class in olorenchemengine.basics) SVC (class in olorenchemengine.basics) SVR (class in olorenchemengine.basics) SwapMutations (class in olorenchemengine.interpret)

T

Tanimoto (class in olorenchemengine.external.GaussianProcess.main) TargetDistDC (class in olorenchemengine.uncertainty) test() (olorenchemengine.base_class.BaseModel method), [1] test_dataset (olorenchemengine.dataset.BaseDataset property) test_oce() (in module olorenchemengine) test_step() (olorenchemengine.beta.gnn.SuperGATModel_beta method) (olorenchemengine.gnn.BaseLightningModule method) TLFromCheckpoint (class in olorenchemengine.gnn) to_json() (olorenchemengine.visualizations.attribute_section.AttributeSection method) (olorenchemengine.visualizations.attribute_section.BaseAttribute method) (olorenchemengine.visualizations.attribute_section.InputThreshold method) (olorenchemengine.visualizations.attribute_section.SimpleAttribute method) to_seq() (olorenchemengine.external.HondaSTRep.operations.Vocab method) (olorenchemengine.external.HondaSTRep.operations.WordVocab method) TOP_MODELS_ADMET() (in module olorenchemengine.manager) TorchGeometricGraph (class in olorenchemengine.representations) TorchMLP (class in olorenchemengine.basics) TorchVocab (class in olorenchemengine.external.HondaSTRep.operations) train() (in module olorenchemengine.external.ChemProp.main) (in module olorenchemengine.external.SPGNN.main) train_dataset (olorenchemengine.dataset.BaseDataset property)

train_word2vec_model() (in module olorenchemengine.external.mol2vec.operations) TrainDistDC (class in olorenchemengine.uncertainty) training_step() (olorenchemengine.beta.gnn.SuperGATModel_beta method) (olorenchemengine.gnn.BaseLightningModule method) trainval_dataset (olorenchemengine.dataset.BaseDataset property) transform() (olorenchemengine.base_class.BaseReduction method), [1] (olorenchemengine.base_class.BaseSKLearnReduction method) (olorenchemengine.dataset.BaseDataset method) (olorenchemengine.dataset.BaseDatasetTransform method) (olorenchemengine.dataset.BaseKFold method) (olorenchemengine.dataset.CleanStructures method) (olorenchemengine.dataset.Discretize method) (olorenchemengine.dataset.KMeansKFold method) (olorenchemengine.dataset.OneHotEncode method) (olorenchemengine.dataset.RandomKFold method) (olorenchemengine.dataset.ScaffoldKFold method) (olorenchemengine.dataset.ScaffoldKMeansKFold method) (olorenchemengine.internal.BasePreprocessor method), [1] (olorenchemengine.internal.LogScaler method) (olorenchemengine.splitters.BaseSplitter method) transformations (olorenchemengine.basics.GuessingRegression attribute) tsne_df() (olorenchemengine.visualizations.visualization.ChemicalSpacePlot method)

U

update_config() (in module olorenchemengine) upload_model() (olorenchemengine.internal.OASConnector method)

upload_oas() (olorenchemengine.base_class.BaseModel method) (olorenchemengine.visualizations.visualization.BaseVisualization method) upload_vis() (olorenchemengine.internal.OASConnector method)

V

valid_dataset (olorenchemengine.dataset.BaseDataset property) validation_step() (olorenchemengine.beta.gnn.SuperGATModel_beta method) (olorenchemengine.gnn.BaseLightningModule method) VisualizationModelManager_Bar (class in olorenchemengine.visualizations.model_comparisons) visualize_morganfp() (olorenchemengine.visualizations.visualization.MorganContributions method) visualize_parameters_ipynb() (olorenchemengine.base_class.BaseModel method) VisualizeADAN (class in olorenchemengine.visualizations.visualization) VisualizeCompounds (class in olorenchemengine.visualizations.visualization) VisualizeCounterfactual (class in olorenchemengine.visualizations.visualization) VisualizeDatasetCompounds (class in olorenchemengine.visualizations.visualization) VisualizeDatasetCV (class in olorenchemengine.visualizations.visualization)

VisualizeDatasetDivision (class in olorenchemengine.visualizations.visualization) VisualizeDatasetSplit (class in olorenchemengine.visualizations.visualization) VisualizeError (class in olorenchemengine.visualizations.visualization) VisualizeFeatures (class in olorenchemengine.visualizations.exploratory_analysis) VisualizeMCS (class in olorenchemengine.visualizations.compounds) VisualizeModelSim (class in olorenchemengine.visualizations.visualization) VisualizeModelSim2 (class in olorenchemengine.visualizations.visualization) VisualizeMoleculePerturbations (class in olorenchemengine.visualizations.visualization) VisualizePredictionSensitivity (class in olorenchemengine.visualizations.visualize_interpret) Vocab (class in olorenchemengine.external.HondaSTRep.operations) vocab_rerank() (olorenchemengine.external.HondaSTRep.operations.TorchVocab method)

W

WordVocab (class in olorenchemengine.external.HondaSTRep.operations)

X

XGBClassifier (class in olorenchemengine.basics)

XGBoostModel (class in olorenchemengine.basics) XGBRegressor (class in olorenchemengine.basics)

Z

ZWK_XGBoostModel (class in olorenchemengine.basics)