Index

_

__call__ (chemprop.utils.ClassRegistry attribute) (chemprop.utils.registry.ClassRegistry attribute) __call__() (chemprop.featurizers.atom.MultiHotAtomFeaturizer method) (chemprop.featurizers.base.Featurizer method) (chemprop.featurizers.BinaryFeaturizerMixin method) (chemprop.featurizers.bond.MultiHotBondFeaturizer method) (chemprop.featurizers.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.CountFeaturizerMixin method) (chemprop.featurizers.Featurizer method) (chemprop.featurizers.molecule.BinaryFeaturizerMixin method) (chemprop.featurizers.molecule.CountFeaturizerMixin method) (chemprop.featurizers.molecule.RDKit2DFeaturizer method) (chemprop.featurizers.molecule.V1RDKit2DFeaturizerMixin method) (chemprop.featurizers.molgraph.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.molgraph.molecule.SimpleMoleculeMolGraphFeaturizer method) (chemprop.featurizers.molgraph.reaction.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.molgraph.SimpleMoleculeMolGraphFeaturizer method) (chemprop.featurizers.MultiHotAtomFeaturizer method) (chemprop.featurizers.MultiHotBondFeaturizer method) (chemprop.featurizers.RDKit2DFeaturizer method) (chemprop.featurizers.SimpleMoleculeMolGraphFeaturizer method) (chemprop.uncertainty.ClassEstimator method) (chemprop.uncertainty.ClassificationDirichletEstimator method) (chemprop.uncertainty.DropoutEstimator method) (chemprop.uncertainty.EnsembleEstimator method) (chemprop.uncertainty.estimator.ClassEstimator method) (chemprop.uncertainty.estimator.ClassificationDirichletEstimator method) (chemprop.uncertainty.estimator.DropoutEstimator method) (chemprop.uncertainty.estimator.EnsembleEstimator method) (chemprop.uncertainty.estimator.EvidentialAleatoricEstimator method) (chemprop.uncertainty.estimator.EvidentialEpistemicEstimator method) (chemprop.uncertainty.estimator.EvidentialTotalEstimator method) (chemprop.uncertainty.estimator.MulticlassDirichletEstimator method) (chemprop.uncertainty.estimator.MVEEstimator method) (chemprop.uncertainty.estimator.NoUncertaintyEstimator method) (chemprop.uncertainty.estimator.QuantileRegressionEstimator method) (chemprop.uncertainty.estimator.UncertaintyEstimator method) (chemprop.uncertainty.EvidentialAleatoricEstimator method) (chemprop.uncertainty.EvidentialEpistemicEstimator method) (chemprop.uncertainty.EvidentialTotalEstimator method) (chemprop.uncertainty.MulticlassDirichletEstimator method) (chemprop.uncertainty.MVEEstimator method) (chemprop.uncertainty.NoUncertaintyEstimator method) (chemprop.uncertainty.QuantileRegressionEstimator method) (chemprop.uncertainty.UncertaintyEstimator method) __getitem__() (chemprop.data.datasets.MoleculeDataset method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.datasets.ReactionDataset method) (chemprop.data.MoleculeDataset method) (chemprop.data.MulticomponentDataset method) (chemprop.data.ReactionDataset method) (chemprop.featurizers.molgraph.cache.MolGraphCache method) (chemprop.featurizers.molgraph.cache.MolGraphCacheOnTheFly method) (chemprop.featurizers.molgraph.MolGraphCache method) (chemprop.featurizers.molgraph.MolGraphCacheOnTheFly method) (chemprop.featurizers.MolGraphCache method) (chemprop.featurizers.MolGraphCacheOnTheFly method)

__iter__() (chemprop.data.ClassBalanceSampler method) (chemprop.data.samplers.ClassBalanceSampler method) (chemprop.data.samplers.SeededSampler method) (chemprop.data.SeededSampler method) __len__() (chemprop.data.BatchMolGraph method) (chemprop.data.ClassBalanceSampler method) (chemprop.data.collate.BatchMolGraph method) (chemprop.data.datapoints.MoleculeDatapoint method) (chemprop.data.datapoints.ReactionDatapoint method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.MoleculeDatapoint method) (chemprop.data.MulticomponentDataset method) (chemprop.data.ReactionDatapoint method) (chemprop.data.samplers.ClassBalanceSampler method) (chemprop.data.samplers.SeededSampler method) (chemprop.data.SeededSampler method) (chemprop.featurizers.atom.MultiHotAtomFeaturizer method) (chemprop.featurizers.bond.MultiHotBondFeaturizer method) (chemprop.featurizers.molecule.MorganFeaturizerMixin method) (chemprop.featurizers.molecule.RDKit2DFeaturizer method) (chemprop.featurizers.molecule.V1RDKit2DFeaturizerMixin method) (chemprop.featurizers.molgraph.cache.MolGraphCache method) (chemprop.featurizers.molgraph.cache.MolGraphCacheOnTheFly method) (chemprop.featurizers.molgraph.MolGraphCache method) (chemprop.featurizers.molgraph.MolGraphCacheOnTheFly method) (chemprop.featurizers.MolGraphCache method) (chemprop.featurizers.MolGraphCacheOnTheFly method) (chemprop.featurizers.MorganFeaturizerMixin method) (chemprop.featurizers.MultiHotAtomFeaturizer method) (chemprop.featurizers.MultiHotBondFeaturizer method) (chemprop.featurizers.RDKit2DFeaturizer method) (chemprop.nn.message_passing.multi.MulticomponentMessagePassing method) (chemprop.nn.message_passing.MulticomponentMessagePassing method) (chemprop.nn.MulticomponentMessagePassing method) __post_init__() (chemprop.data.BatchMolGraph method) (chemprop.data.collate.BatchMolGraph method) (chemprop.data.datapoints.MoleculeDatapoint method) (chemprop.data.datapoints.ReactionDatapoint method) (chemprop.data.datasets.MoleculeDataset method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.datasets.ReactionDataset method) (chemprop.data.MoleculeDatapoint method) (chemprop.data.MoleculeDataset method) (chemprop.data.MulticomponentDataset method) (chemprop.data.ReactionDatapoint method) (chemprop.data.ReactionDataset method) (chemprop.featurizers.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.molgraph.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.molgraph.molecule.SimpleMoleculeMolGraphFeaturizer method) (chemprop.featurizers.molgraph.reaction.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.molgraph.SimpleMoleculeMolGraphFeaturizer method) (chemprop.featurizers.SimpleMoleculeMolGraphFeaturizer method) __repr__() (chemprop.utils.ClassRegistry method) (chemprop.utils.registry.ClassRegistry method) __str__() (chemprop.utils.ClassRegistry method) (chemprop.utils.registry.ClassRegistry method)

A

Activation (class in chemprop.nn) (class in chemprop.nn.utils) AdaptiveMulticlassConformalCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) agg (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) Aggregation (class in chemprop.nn) (class in chemprop.nn.agg) AggregationRegistry (in module chemprop.nn) (in module chemprop.nn.agg) alpha (chemprop.nn.metrics.QuantileLoss attribute) (chemprop.nn.QuantileLoss attribute) (chemprop.uncertainty.calibrator.MulticlassConformalCalibrator attribute) (chemprop.uncertainty.calibrator.MultilabelConformalCalibrator attribute) (chemprop.uncertainty.calibrator.RegressionConformalCalibrator attribute) (chemprop.uncertainty.MulticlassConformalCalibrator attribute) (chemprop.uncertainty.MultilabelConformalCalibrator attribute) (chemprop.uncertainty.RegressionConformalCalibrator attribute) apply() (chemprop.uncertainty.calibrator.CalibratorBase method) (chemprop.uncertainty.calibrator.IsotonicCalibrator method) (chemprop.uncertainty.calibrator.IsotonicMulticlassCalibrator method) (chemprop.uncertainty.calibrator.MulticlassConformalCalibrator method) (chemprop.uncertainty.calibrator.MultilabelConformalCalibrator method) (chemprop.uncertainty.calibrator.MVEWeightingCalibrator method) (chemprop.uncertainty.calibrator.PlattCalibrator method) (chemprop.uncertainty.calibrator.RegressionConformalCalibrator method) (chemprop.uncertainty.calibrator.ZelikmanCalibrator method) (chemprop.uncertainty.calibrator.ZScalingCalibrator method) (chemprop.uncertainty.CalibratorBase method) (chemprop.uncertainty.IsotonicCalibrator method) (chemprop.uncertainty.IsotonicMulticlassCalibrator method) (chemprop.uncertainty.MulticlassConformalCalibrator method) (chemprop.uncertainty.MultilabelConformalCalibrator method) (chemprop.uncertainty.MVEWeightingCalibrator method) (chemprop.uncertainty.PlattCalibrator method) (chemprop.uncertainty.RegressionConformalCalibrator method) (chemprop.uncertainty.ZelikmanCalibrator method) (chemprop.uncertainty.ZScalingCalibrator method)

AtomFeatureMode (class in chemprop.featurizers) (class in chemprop.featurizers.atom) atomic_nums (chemprop.featurizers.atom.MultiHotAtomFeaturizer attribute) (chemprop.featurizers.MultiHotAtomFeaturizer attribute) AtomMessagePassing (class in chemprop.nn) (class in chemprop.nn.message_passing) (class in chemprop.nn.message_passing.base) AttentiveAggregation (class in chemprop.nn) (class in chemprop.nn.agg) author (in module conf) autoapi_dirs (in module conf) autoapi_file_patterns (in module conf) autoapi_ignore (in module conf) autoapi_keep_files (in module conf) autoapi_options (in module conf) autodoc_typehints (in module conf)

B

batch (chemprop.data.BatchMolGraph attribute) (chemprop.data.collate.BatchMolGraph attribute) BatchMolGraph (class in chemprop.data) (class in chemprop.data.collate) BCELoss (class in chemprop.nn) (class in chemprop.nn.metrics) bibtex_bibfiles (in module conf) BinaryAccuracy (class in chemprop.nn) (class in chemprop.nn.metrics) BinaryAUPRC (class in chemprop.nn) (class in chemprop.nn.metrics) BinaryAUROC (class in chemprop.nn) (class in chemprop.nn.metrics) BinaryClassificationCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) BinaryClassificationEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) BinaryClassificationFFN (class in chemprop.nn) (class in chemprop.nn.predictors) BinaryClassificationFFNBase (class in chemprop.nn) (class in chemprop.nn.predictors) BinaryDirichletFFN (class in chemprop.nn) (class in chemprop.nn.predictors) BinaryF1Score (class in chemprop.nn) (class in chemprop.nn.metrics) BinaryFeaturizerMixin (class in chemprop.featurizers) (class in chemprop.featurizers.molecule) BinaryMCCLoss (class in chemprop.nn) (class in chemprop.nn.metrics) BinaryMCCMetric (class in chemprop.nn) (class in chemprop.nn.metrics)

blocks (chemprop.nn.message_passing.multi.MulticomponentMessagePassing attribute) (chemprop.nn.message_passing.MulticomponentMessagePassing attribute) (chemprop.nn.MulticomponentMessagePassing attribute) bmg (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.TrainingBatch attribute) bmgs (chemprop.data.collate.MulticomponentTrainingBatch attribute) bn (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) bond_types (chemprop.featurizers.bond.MultiHotBondFeaturizer attribute) (chemprop.featurizers.MultiHotBondFeaturizer attribute) BondMessagePassing (class in chemprop.nn) (class in chemprop.nn.message_passing) (class in chemprop.nn.message_passing.base) BoundedMAE (class in chemprop.nn) (class in chemprop.nn.metrics) BoundedMixin (class in chemprop.nn) (class in chemprop.nn.metrics) BoundedMSE (class in chemprop.nn) (class in chemprop.nn.metrics) BoundedRMSE (class in chemprop.nn) (class in chemprop.nn.metrics) bounds (chemprop.uncertainty.calibrator.RegressionConformalCalibrator attribute) (chemprop.uncertainty.RegressionConformalCalibrator attribute) build() (chemprop.nn.ffn.MLP class method) (chemprop.utils.Factory class method) (chemprop.utils.registry.Factory class method) build_dataloader() (in module chemprop.data) (in module chemprop.data.dataloader) build_NoamLike_LRSched() (in module chemprop.schedulers)

C

cache (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.datasets.ReactionDataset property) (chemprop.data.MoleculeDataset property) (chemprop.data.ReactionDataset property) CalibrationAreaEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) CalibratorBase (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) CGRFeaturizer (in module chemprop.featurizers) (in module chemprop.featurizers.molgraph) (in module chemprop.featurizers.molgraph.reaction) chemprop module chemprop.conf module chemprop.data module chemprop.data.collate module chemprop.data.dataloader module chemprop.data.datapoints module chemprop.data.datasets module chemprop.data.molgraph module chemprop.data.samplers module chemprop.data.splitting module chemprop.exceptions module chemprop.featurizers module chemprop.featurizers.atom module chemprop.featurizers.base module chemprop.featurizers.bond module chemprop.featurizers.molecule module chemprop.featurizers.molgraph module chemprop.featurizers.molgraph.cache module chemprop.featurizers.molgraph.mixins module chemprop.featurizers.molgraph.molecule module chemprop.featurizers.molgraph.reaction module chemprop.models module chemprop.models.model module chemprop.models.multi module chemprop.models.utils module chemprop.nn module chemprop.nn.agg module chemprop.nn.ffn module chemprop.nn.hparams module chemprop.nn.message_passing module chemprop.nn.message_passing.base module chemprop.nn.message_passing.multi module chemprop.nn.message_passing.proto module chemprop.nn.metrics module chemprop.nn.predictors module

chemprop.nn.transforms module chemprop.nn.utils module chemprop.schedulers module chemprop.types module chemprop.uncertainty module chemprop.uncertainty.calibrator module chemprop.uncertainty.estimator module chemprop.uncertainty.evaluator module chemprop.utils module chemprop.utils.registry module chemprop.utils.utils module chemprop.utils.v1_to_v2 module chemprop.utils.v2_0_to_v2_1 module ChempropMetric (class in chemprop.nn) (class in chemprop.nn.metrics) chiral_tags (chemprop.featurizers.atom.MultiHotAtomFeaturizer attribute) (chemprop.featurizers.MultiHotAtomFeaturizer attribute) ClassBalanceSampler (class in chemprop.data) (class in chemprop.data.samplers) ClassEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) ClassificationDirichletEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) ClassificationMixin (class in chemprop.nn) (class in chemprop.nn.metrics) ClassRegistry (class in chemprop.utils) (class in chemprop.utils.registry) cls (chemprop.nn.hparams.HParamsDict attribute) collate_batch() (in module chemprop.data) (in module chemprop.data.collate) collate_multicomponent() (in module chemprop.data) (in module chemprop.data.collate) compute() (chemprop.nn.BinaryAUPRC method) (chemprop.nn.BinaryMCCLoss method) (chemprop.nn.BinaryMCCMetric method) (chemprop.nn.ChempropMetric method) (chemprop.nn.metrics.BinaryAUPRC method) (chemprop.nn.metrics.BinaryMCCLoss method) (chemprop.nn.metrics.BinaryMCCMetric method) (chemprop.nn.metrics.ChempropMetric method) (chemprop.nn.metrics.MulticlassMCCLoss method) (chemprop.nn.metrics.MulticlassMCCMetric method) (chemprop.nn.metrics.RMSE method) (chemprop.nn.MulticlassMCCLoss method) (chemprop.nn.MulticlassMCCMetric method) (chemprop.nn.RMSE method) CondensedGraphOfReactionFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.molgraph) (class in chemprop.featurizers.molgraph.reaction) conf module configure_optimizers() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) convert_hyper_parameters_v1_to_v2() (in module chemprop.utils.v1_to_v2) convert_model_dict_v1_to_v2() (in module chemprop.utils.v1_to_v2) convert_model_file_v1_to_v2() (in module chemprop.utils.v1_to_v2) convert_state_dict_v1_to_v2() (in module chemprop.utils.v1_to_v2) copyright (in module conf) CountFeaturizerMixin (class in chemprop.featurizers) (class in chemprop.featurizers.molecule) criterion (chemprop.models.model.MPNN property) (chemprop.models.MPNN property) (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.Predictor attribute) CrossEntropyLoss (class in chemprop.nn) (class in chemprop.nn.metrics)

D

d_ef (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.datasets.MulticomponentDataset property) (chemprop.data.datasets.ReactionDataset property) (chemprop.data.MoleculeDataset property) (chemprop.data.MulticomponentDataset property) (chemprop.data.ReactionDataset property) d_vd (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.datasets.MulticomponentDataset property) (chemprop.data.datasets.ReactionDataset property) (chemprop.data.MoleculeDataset property) (chemprop.data.MulticomponentDataset property) (chemprop.data.ReactionDataset property) d_vf (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.datasets.MulticomponentDataset property) (chemprop.data.datasets.ReactionDataset property) (chemprop.data.MoleculeDataset property) (chemprop.data.MulticomponentDataset property) (chemprop.data.ReactionDataset property) d_xd (chemprop.data.datasets.MulticomponentDataset property) (chemprop.data.MulticomponentDataset property)

data (chemprop.data.datasets.MoleculeDataset attribute) (chemprop.data.datasets.ReactionDataset attribute) (chemprop.data.MoleculeDataset attribute) (chemprop.data.ReactionDataset attribute) Datapoints (in module chemprop.data.splitting) datasets (chemprop.data.datasets.MulticomponentDataset attribute) (chemprop.data.MulticomponentDataset attribute) Datum (class in chemprop.data) (class in chemprop.data.datasets) DEFAULT_HIDDEN_DIM (in module chemprop.conf) degrees (chemprop.featurizers.atom.MultiHotAtomFeaturizer attribute) (chemprop.featurizers.MultiHotAtomFeaturizer attribute) dim (chemprop.nn.agg.Aggregation attribute) (chemprop.nn.Aggregation attribute) DirichletLoss (class in chemprop.nn) (class in chemprop.nn.metrics) dropout (chemprop.uncertainty.DropoutEstimator attribute) (chemprop.uncertainty.estimator.DropoutEstimator attribute) DropoutEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator)

E

E (chemprop.data.BatchMolGraph attribute) (chemprop.data.collate.BatchMolGraph attribute) (chemprop.data.MolGraph attribute) (chemprop.data.molgraph.MolGraph attribute) E_f (chemprop.data.datapoints.MoleculeDatapoint attribute) (chemprop.data.MoleculeDatapoint attribute) E_fs (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.MoleculeDataset property) E_transform (chemprop.nn.GraphTransform attribute) (chemprop.nn.transforms.GraphTransform attribute) edge_index (chemprop.data.BatchMolGraph attribute) (chemprop.data.collate.BatchMolGraph attribute) (chemprop.data.MolGraph attribute) (chemprop.data.molgraph.MolGraph attribute) ELU (chemprop.nn.Activation attribute) (chemprop.nn.utils.Activation attribute) encode() (chemprop.nn.Predictor method) (chemprop.nn.predictors.Predictor method) encoding() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) ensemble_size (chemprop.uncertainty.DropoutEstimator attribute) (chemprop.uncertainty.estimator.DropoutEstimator attribute) EnsembleEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) EnumMapping (class in chemprop.utils) (class in chemprop.utils.utils) eps (chemprop.nn.EvidentialLoss attribute) (chemprop.nn.metrics.EvidentialLoss attribute) evaluate() (chemprop.uncertainty.BinaryClassificationEvaluator method) (chemprop.uncertainty.CalibrationAreaEvaluator method) (chemprop.uncertainty.evaluator.BinaryClassificationEvaluator method) (chemprop.uncertainty.evaluator.CalibrationAreaEvaluator method) (chemprop.uncertainty.evaluator.ExpectedNormalizedErrorEvaluator method) (chemprop.uncertainty.evaluator.MulticlassClassificationEvaluator method) (chemprop.uncertainty.evaluator.MulticlassConformalEvaluator method) (chemprop.uncertainty.evaluator.MultilabelConformalEvaluator method) (chemprop.uncertainty.evaluator.NLLClassEvaluator method) (chemprop.uncertainty.evaluator.NLLMulticlassEvaluator method) (chemprop.uncertainty.evaluator.NLLRegressionEvaluator method) (chemprop.uncertainty.evaluator.RegressionConformalEvaluator method) (chemprop.uncertainty.evaluator.RegressionEvaluator method) (chemprop.uncertainty.evaluator.SpearmanEvaluator method) (chemprop.uncertainty.ExpectedNormalizedErrorEvaluator method) (chemprop.uncertainty.MulticlassClassificationEvaluator method) (chemprop.uncertainty.MulticlassConformalEvaluator method) (chemprop.uncertainty.MultilabelConformalEvaluator method) (chemprop.uncertainty.NLLClassEvaluator method) (chemprop.uncertainty.NLLMulticlassEvaluator method) (chemprop.uncertainty.NLLRegressionEvaluator method) (chemprop.uncertainty.RegressionConformalEvaluator method) (chemprop.uncertainty.RegressionEvaluator method) (chemprop.uncertainty.SpearmanEvaluator method)

EvidentialAleatoricEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) EvidentialEpistemicEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) EvidentialFFN (class in chemprop.nn) (class in chemprop.nn.predictors) EvidentialLoss (class in chemprop.nn) (class in chemprop.nn.metrics) EvidentialTotalEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) exclude_patterns (in module conf) ExpectedNormalizedErrorEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) extensions (in module conf) extra_atom_fdim (chemprop.featurizers.molgraph.molecule.SimpleMoleculeMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.SimpleMoleculeMolGraphFeaturizer attribute) (chemprop.featurizers.SimpleMoleculeMolGraphFeaturizer attribute) extra_bond_fdim (chemprop.featurizers.molgraph.molecule.SimpleMoleculeMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.SimpleMoleculeMolGraphFeaturizer attribute) (chemprop.featurizers.SimpleMoleculeMolGraphFeaturizer attribute) extra_repr() (chemprop.nn.ChempropMetric method) (chemprop.nn.DirichletLoss method) (chemprop.nn.EvidentialLoss method) (chemprop.nn.metrics.ChempropMetric method) (chemprop.nn.metrics.DirichletLoss method) (chemprop.nn.metrics.EvidentialLoss method) (chemprop.nn.metrics.QuantileLoss method) (chemprop.nn.metrics.SID method) (chemprop.nn.metrics.Wasserstein method) (chemprop.nn.QuantileLoss method) (chemprop.nn.SID method) (chemprop.nn.Wasserstein method)

F

F (chemprop.featurizers.molecule.MorganFeaturizerMixin attribute) (chemprop.featurizers.MorganFeaturizerMixin attribute) Factory (class in chemprop.utils) (class in chemprop.utils.registry) featurizer (chemprop.data.datasets.MoleculeDataset attribute) (chemprop.data.datasets.ReactionDataset attribute) (chemprop.data.MoleculeDataset attribute) (chemprop.data.ReactionDataset attribute) Featurizer (class in chemprop.featurizers) (class in chemprop.featurizers.base) FFN (class in chemprop.nn.ffn) final_lr (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) find_class() (chemprop.utils.v2_0_to_v2_1.Unpickler method) fingerprint() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) (chemprop.models.multi.MulticomponentMPNN method) (chemprop.models.MulticomponentMPNN method) fit() (chemprop.uncertainty.BinaryClassificationCalibrator method) (chemprop.uncertainty.calibrator.BinaryClassificationCalibrator method) (chemprop.uncertainty.calibrator.CalibratorBase method) (chemprop.uncertainty.calibrator.IsotonicCalibrator method) (chemprop.uncertainty.calibrator.IsotonicMulticlassCalibrator method) (chemprop.uncertainty.calibrator.MulticlassClassificationCalibrator method) (chemprop.uncertainty.calibrator.MulticlassConformalCalibrator method) (chemprop.uncertainty.calibrator.MultilabelConformalCalibrator method) (chemprop.uncertainty.calibrator.MVEWeightingCalibrator method) (chemprop.uncertainty.calibrator.PlattCalibrator method) (chemprop.uncertainty.calibrator.RegressionCalibrator method) (chemprop.uncertainty.calibrator.RegressionConformalCalibrator method) (chemprop.uncertainty.calibrator.ZelikmanCalibrator method) (chemprop.uncertainty.calibrator.ZScalingCalibrator method) (chemprop.uncertainty.CalibratorBase method) (chemprop.uncertainty.IsotonicCalibrator method) (chemprop.uncertainty.IsotonicMulticlassCalibrator method) (chemprop.uncertainty.MulticlassClassificationCalibrator method) (chemprop.uncertainty.MulticlassConformalCalibrator method) (chemprop.uncertainty.MultilabelConformalCalibrator method) (chemprop.uncertainty.MVEWeightingCalibrator method) (chemprop.uncertainty.PlattCalibrator method) (chemprop.uncertainty.RegressionCalibrator method) (chemprop.uncertainty.RegressionConformalCalibrator method) (chemprop.uncertainty.ZelikmanCalibrator method) (chemprop.uncertainty.ZScalingCalibrator method) formal_charges (chemprop.featurizers.atom.MultiHotAtomFeaturizer attribute) (chemprop.featurizers.MultiHotAtomFeaturizer attribute)

forward() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) (chemprop.nn.agg.Aggregation method) (chemprop.nn.agg.AttentiveAggregation method) (chemprop.nn.agg.MeanAggregation method) (chemprop.nn.agg.NormAggregation method) (chemprop.nn.agg.SumAggregation method) (chemprop.nn.Aggregation method) (chemprop.nn.AttentiveAggregation method) (chemprop.nn.BinaryClassificationFFN method) (chemprop.nn.BinaryDirichletFFN method) (chemprop.nn.EvidentialFFN method) (chemprop.nn.ffn.FFN method) (chemprop.nn.GraphTransform method) (chemprop.nn.MeanAggregation method) (chemprop.nn.message_passing.MessagePassing method) (chemprop.nn.message_passing.multi.MulticomponentMessagePassing method) (chemprop.nn.message_passing.MulticomponentMessagePassing method) (chemprop.nn.message_passing.proto.MessagePassing method) (chemprop.nn.MessagePassing method) (chemprop.nn.MulticlassClassificationFFN method) (chemprop.nn.MulticomponentMessagePassing method) (chemprop.nn.MveFFN method) (chemprop.nn.NormAggregation method) (chemprop.nn.Predictor method) (chemprop.nn.predictors.BinaryClassificationFFN method) (chemprop.nn.predictors.BinaryDirichletFFN method) (chemprop.nn.predictors.EvidentialFFN method) (chemprop.nn.predictors.MulticlassClassificationFFN method) (chemprop.nn.predictors.MulticlassDirichletFFN method) (chemprop.nn.predictors.MveFFN method) (chemprop.nn.predictors.Predictor method) (chemprop.nn.predictors.RegressionFFN method) (chemprop.nn.predictors.SpectralFFN method) (chemprop.nn.QuantileFFN method) (chemprop.nn.RegressionFFN method) (chemprop.nn.ScaleTransform method) (chemprop.nn.SpectralFFN method) (chemprop.nn.SumAggregation method) (chemprop.nn.transforms.GraphTransform method) (chemprop.nn.transforms.ScaleTransform method) (chemprop.nn.transforms.UnscaleTransform method) (chemprop.nn.UnscaleTransform method) from_hparams() (in module chemprop.nn.hparams) full_state_update (chemprop.nn.ChempropMetric attribute) (chemprop.nn.metrics.ChempropMetric attribute)

G

generator (chemprop.featurizers.molecule.V1RDKit2DFeaturizer attribute) (chemprop.featurizers.molecule.V1RDKit2DNormalizedFeaturizer attribute) (chemprop.featurizers.V1RDKit2DFeaturizer attribute) (chemprop.featurizers.V1RDKit2DNormalizedFeaturizer attribute) get() (chemprop.utils.EnumMapping class method) (chemprop.utils.utils.EnumMapping class method) get_activation_function() (in module chemprop.nn.utils) get_multi_hot_atom_featurizer() (in module chemprop.featurizers) (in module chemprop.featurizers.atom)

GraphFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.base) GraphTransform (class in chemprop.nn) (class in chemprop.nn.transforms) gt_mask (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute) (chemprop.data.TrainingBatch attribute)

H

HasHParams (class in chemprop.nn.hparams) higher_is_better (chemprop.nn.ChempropMetric attribute) (chemprop.nn.metrics.ChempropMetric attribute) hparams (chemprop.nn.agg.Aggregation attribute) (chemprop.nn.Aggregation attribute) (chemprop.nn.hparams.HasHParams attribute) (chemprop.nn.message_passing.multi.MulticomponentMessagePassing attribute) (chemprop.nn.message_passing.MulticomponentMessagePassing attribute) (chemprop.nn.MulticomponentMessagePassing attribute)

HParamsDict (class in chemprop.nn.hparams) html_static_path (in module conf) html_theme (in module conf) hybridizations (chemprop.featurizers.atom.MultiHotAtomFeaturizer attribute) (chemprop.featurizers.MultiHotAtomFeaturizer attribute)

I

idxs (chemprop.data.samplers.SeededSampler attribute) (chemprop.data.SeededSampler attribute) init_lr (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) initialize() (chemprop.nn.AtomMessagePassing method) (chemprop.nn.BondMessagePassing method) (chemprop.nn.message_passing.AtomMessagePassing method) (chemprop.nn.message_passing.base.AtomMessagePassing method) (chemprop.nn.message_passing.base.BondMessagePassing method) (chemprop.nn.message_passing.BondMessagePassing method) input_dim (chemprop.nn.ffn.FFN attribute) (chemprop.nn.ffn.MLP property) (chemprop.nn.message_passing.MessagePassing attribute) (chemprop.nn.message_passing.proto.MessagePassing attribute) (chemprop.nn.MessagePassing attribute) (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.Predictor attribute)

InvalidShapeError is_differentiable (chemprop.nn.ChempropMetric attribute) (chemprop.nn.metrics.ChempropMetric attribute) IsotonicCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) IsotonicMulticlassCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) items() (chemprop.utils.EnumMapping class method) (chemprop.utils.utils.EnumMapping class method)

K

KENNARD_STONE (chemprop.data.splitting.SplitType attribute) (chemprop.data.SplitType attribute) keys() (chemprop.utils.EnumMapping class method) (chemprop.utils.utils.EnumMapping class method)

KMEANS (chemprop.data.splitting.SplitType attribute) (chemprop.data.SplitType attribute)

L

LEAKYRELU (chemprop.nn.Activation attribute) (chemprop.nn.utils.Activation attribute) length (chemprop.data.ClassBalanceSampler attribute) (chemprop.data.samplers.ClassBalanceSampler attribute) (chemprop.featurizers.molecule.MorganFeaturizerMixin attribute) (chemprop.featurizers.MorganFeaturizerMixin attribute) load_from_checkpoint() (chemprop.models.model.MPNN class method) (chemprop.models.MPNN class method) load_from_file() (chemprop.models.model.MPNN class method) (chemprop.models.MPNN class method) load_model() (in module chemprop.models) (in module chemprop.models.utils) load_output_columns() (in module chemprop.models.utils)

logger (in module chemprop.data.dataloader) (in module chemprop.data.splitting) (in module chemprop.featurizers.molecule) (in module chemprop.featurizers.molgraph.reaction) (in module chemprop.models.model) (in module chemprop.nn.message_passing.multi) (in module chemprop.uncertainty.calibrator) LossFunctionRegistry (in module chemprop.nn) (in module chemprop.nn.metrics) lt_mask (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute) (chemprop.data.TrainingBatch attribute)

M

MAE (class in chemprop.nn) (class in chemprop.nn.metrics) make_mol() (in module chemprop.utils) (in module chemprop.utils.utils) make_split_indices() (in module chemprop.data) (in module chemprop.data.splitting) map_reac_to_prod() (chemprop.featurizers.CondensedGraphOfReactionFeaturizer class method) (chemprop.featurizers.molgraph.CondensedGraphOfReactionFeaturizer class method) (chemprop.featurizers.molgraph.reaction.CondensedGraphOfReactionFeaturizer class method) max_lr (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) MeanAggregation (class in chemprop.nn) (class in chemprop.nn.agg) message() (chemprop.nn.AtomMessagePassing method) (chemprop.nn.BondMessagePassing method) (chemprop.nn.message_passing.AtomMessagePassing method) (chemprop.nn.message_passing.base.AtomMessagePassing method) (chemprop.nn.message_passing.base.BondMessagePassing method) (chemprop.nn.message_passing.BondMessagePassing method) message_passing (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) (chemprop.models.multi.MulticomponentMPNN attribute) (chemprop.models.MulticomponentMPNN attribute) MessagePassing (class in chemprop.nn) (class in chemprop.nn.message_passing) (class in chemprop.nn.message_passing.proto) MetricRegistry (in module chemprop.nn) (in module chemprop.nn.metrics) metrics (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) mg (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute) mgs (chemprop.data.BatchMolGraph attribute) (chemprop.data.collate.BatchMolGraph attribute) MLP (class in chemprop.nn.ffn) mode (chemprop.featurizers.CondensedGraphOfReactionFeaturizer property) (chemprop.featurizers.molgraph.CondensedGraphOfReactionFeaturizer property) (chemprop.featurizers.molgraph.reaction.CondensedGraphOfReactionFeaturizer property) mode_ (chemprop.featurizers.CondensedGraphOfReactionFeaturizer attribute) (chemprop.featurizers.molgraph.CondensedGraphOfReactionFeaturizer attribute) (chemprop.featurizers.molgraph.reaction.CondensedGraphOfReactionFeaturizer attribute) model (in module chemprop.utils.v2_0_to_v2_1) module chemprop chemprop.conf chemprop.data chemprop.data.collate chemprop.data.dataloader chemprop.data.datapoints chemprop.data.datasets chemprop.data.molgraph chemprop.data.samplers chemprop.data.splitting chemprop.exceptions chemprop.featurizers chemprop.featurizers.atom chemprop.featurizers.base chemprop.featurizers.bond chemprop.featurizers.molecule chemprop.featurizers.molgraph chemprop.featurizers.molgraph.cache chemprop.featurizers.molgraph.mixins chemprop.featurizers.molgraph.molecule chemprop.featurizers.molgraph.reaction chemprop.models chemprop.models.model chemprop.models.multi chemprop.models.utils chemprop.nn chemprop.nn.agg chemprop.nn.ffn chemprop.nn.hparams chemprop.nn.message_passing chemprop.nn.message_passing.base chemprop.nn.message_passing.multi chemprop.nn.message_passing.proto chemprop.nn.metrics chemprop.nn.predictors chemprop.nn.transforms chemprop.nn.utils chemprop.schedulers chemprop.types chemprop.uncertainty chemprop.uncertainty.calibrator chemprop.uncertainty.estimator chemprop.uncertainty.evaluator chemprop.utils chemprop.utils.registry chemprop.utils.utils chemprop.utils.v1_to_v2 chemprop.utils.v2_0_to_v2_1 conf

MoleculeDatapoint (class in chemprop.data) (class in chemprop.data.datapoints) MoleculeDataset (class in chemprop.data) (class in chemprop.data.datasets) MoleculeFeaturizer (in module chemprop.data.datapoints) MoleculeFeaturizerRegistry (in module chemprop.featurizers) (in module chemprop.featurizers.molecule) MolGraph (class in chemprop.data) (class in chemprop.data.molgraph) MolGraphCache (class in chemprop.featurizers) (class in chemprop.featurizers.molgraph) (class in chemprop.featurizers.molgraph.cache) MolGraphCacheFacade (class in chemprop.featurizers) (class in chemprop.featurizers.molgraph) (class in chemprop.featurizers.molgraph.cache) MolGraphCacheOnTheFly (class in chemprop.featurizers) (class in chemprop.featurizers.molgraph) (class in chemprop.featurizers.molgraph.cache) MolGraphDataset (in module chemprop.data) (in module chemprop.data.datasets) mols (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.datasets.MulticomponentDataset property) (chemprop.data.datasets.ReactionDataset property) (chemprop.data.MoleculeDataset property) (chemprop.data.MulticomponentDataset property) (chemprop.data.ReactionDataset property) MorganBinaryFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.molecule) MorganCountFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.molecule) MorganFeaturizerMixin (class in chemprop.featurizers) (class in chemprop.featurizers.molecule) MPNN (class in chemprop.models) (class in chemprop.models.model) MSE (class in chemprop.nn) (class in chemprop.nn.metrics) MulticlassClassificationCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) MulticlassClassificationEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) MulticlassClassificationFFN (class in chemprop.nn) (class in chemprop.nn.predictors) MulticlassConformalCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) MulticlassConformalEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) MulticlassDirichletEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) MulticlassDirichletFFN (class in chemprop.nn.predictors) MulticlassMCCLoss (class in chemprop.nn) (class in chemprop.nn.metrics) MulticlassMCCMetric (class in chemprop.nn) (class in chemprop.nn.metrics) MulticomponentDatapoints (in module chemprop.data.splitting) MulticomponentDataset (class in chemprop.data) (class in chemprop.data.datasets) MulticomponentMessagePassing (class in chemprop.nn) (class in chemprop.nn.message_passing) (class in chemprop.nn.message_passing.multi) MulticomponentMPNN (class in chemprop.models) (class in chemprop.models.multi) MulticomponentTrainingBatch (class in chemprop.data.collate) MultiHotAtomFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.atom) MultiHotBondFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.bond) MultilabelConformalCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) MultilabelConformalEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) MVEEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) MveFFN (class in chemprop.nn) (class in chemprop.nn.predictors) MVELoss (class in chemprop.nn) (class in chemprop.nn.metrics) MVEWeightingCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator)

N

n_classes (chemprop.nn.MulticlassClassificationFFN attribute) (chemprop.nn.predictors.MulticlassClassificationFFN attribute) n_components (chemprop.data.datasets.MulticomponentDataset property) (chemprop.data.MulticomponentDataset property) (chemprop.nn.message_passing.multi.MulticomponentMessagePassing attribute) (chemprop.nn.message_passing.MulticomponentMessagePassing attribute) (chemprop.nn.MulticomponentMessagePassing attribute) n_targets (chemprop.models.model.MPNN property) (chemprop.models.MPNN property) (chemprop.nn.BinaryClassificationFFN attribute) (chemprop.nn.BinaryDirichletFFN attribute) (chemprop.nn.EvidentialFFN attribute) (chemprop.nn.MulticlassClassificationFFN attribute) (chemprop.nn.MveFFN attribute) (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.BinaryClassificationFFN attribute) (chemprop.nn.predictors.BinaryDirichletFFN attribute) (chemprop.nn.predictors.EvidentialFFN attribute) (chemprop.nn.predictors.MulticlassClassificationFFN attribute) (chemprop.nn.predictors.MveFFN attribute) (chemprop.nn.predictors.Predictor attribute) (chemprop.nn.predictors.RegressionFFN attribute) (chemprop.nn.predictors.SpectralFFN attribute) (chemprop.nn.QuantileFFN attribute) (chemprop.nn.RegressionFFN attribute) (chemprop.nn.SpectralFFN attribute) n_tasks (chemprop.models.model.MPNN property) (chemprop.models.MPNN property) (chemprop.nn.MulticlassClassificationFFN property) (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.MulticlassClassificationFFN property) (chemprop.nn.predictors.Predictor attribute) name_mappings (chemprop.utils.v2_0_to_v2_1.Unpickler attribute)

names (chemprop.data.datasets.MulticomponentDataset property) (chemprop.data.MulticomponentDataset property) nbsphinx_allow_errors (in module conf) nbsphinx_execute (in module conf) neg_idxs (chemprop.data.ClassBalanceSampler attribute) (chemprop.data.samplers.ClassBalanceSampler attribute) NLLClassEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) NLLMulticlassEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) NLLRegressionEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) nonconformity_scores() (chemprop.uncertainty.AdaptiveMulticlassConformalCalibrator static method) (chemprop.uncertainty.calibrator.AdaptiveMulticlassConformalCalibrator static method) (chemprop.uncertainty.calibrator.MulticlassConformalCalibrator static method) (chemprop.uncertainty.calibrator.MultilabelConformalCalibrator static method) (chemprop.uncertainty.MulticlassConformalCalibrator static method) (chemprop.uncertainty.MultilabelConformalCalibrator static method) norm (chemprop.nn.agg.NormAggregation attribute) (chemprop.nn.NormAggregation attribute) NormAggregation (class in chemprop.nn) (class in chemprop.nn.agg) normalize_inputs() (chemprop.data.datasets.MoleculeDataset method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.MoleculeDataset method) (chemprop.data.MulticomponentDataset method) normalize_targets() (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.MulticomponentDataset method) NoUncertaintyEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) num_Hs (chemprop.featurizers.atom.MultiHotAtomFeaturizer attribute) (chemprop.featurizers.MultiHotAtomFeaturizer attribute) num_only() (chemprop.featurizers.atom.MultiHotAtomFeaturizer method) (chemprop.featurizers.MultiHotAtomFeaturizer method)

O

on_validation_model_eval() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) (chemprop.models.multi.MulticomponentMPNN method) (chemprop.models.MulticomponentMPNN method) one_hot_index() (chemprop.featurizers.bond.MultiHotBondFeaturizer class method) (chemprop.featurizers.MultiHotBondFeaturizer class method) ORGANIC (chemprop.featurizers.atom.AtomFeatureMode attribute) (chemprop.featurizers.AtomFeatureMode attribute) organic() (chemprop.featurizers.atom.MultiHotAtomFeaturizer class method) (chemprop.featurizers.MultiHotAtomFeaturizer class method) output_dim (chemprop.models.model.MPNN property) (chemprop.models.MPNN property) (chemprop.nn.ffn.FFN attribute) (chemprop.nn.ffn.MLP property) (chemprop.nn.message_passing.MessagePassing attribute) (chemprop.nn.message_passing.multi.MulticomponentMessagePassing property) (chemprop.nn.message_passing.MulticomponentMessagePassing property) (chemprop.nn.message_passing.proto.MessagePassing attribute) (chemprop.nn.MessagePassing attribute) (chemprop.nn.MulticomponentMessagePassing property) (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.Predictor attribute)

output_transform (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.Predictor attribute)

P

p (chemprop.uncertainty.calibrator.ZelikmanCalibrator attribute) (chemprop.uncertainty.ZelikmanCalibrator attribute) PlattCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) pos_idxs (chemprop.data.ClassBalanceSampler attribute) (chemprop.data.samplers.ClassBalanceSampler attribute) predict_step() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) predictor (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) Predictor (class in chemprop.nn) (class in chemprop.nn.predictors)

PredictorRegistry (in module chemprop.nn) (in module chemprop.nn.predictors) PRELU (chemprop.nn.Activation attribute) (chemprop.nn.utils.Activation attribute) pretty_shape() (in module chemprop.utils) (in module chemprop.utils.utils) PROD_DIFF (chemprop.featurizers.molgraph.reaction.RxnMode attribute) (chemprop.featurizers.molgraph.RxnMode attribute) (chemprop.featurizers.RxnMode attribute) PROD_DIFF_BALANCE (chemprop.featurizers.molgraph.reaction.RxnMode attribute) (chemprop.featurizers.molgraph.RxnMode attribute) (chemprop.featurizers.RxnMode attribute) project (in module conf)

Q

QuantileFFN (class in chemprop.nn) QuantileLoss (class in chemprop.nn) (class in chemprop.nn.metrics)

QuantileRegressionEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator)

R

R2Score (class in chemprop.nn) (class in chemprop.nn.metrics) RANDOM (chemprop.data.splitting.SplitType attribute) (chemprop.data.SplitType attribute) RANDOM_WITH_REPEATED_SMILES (chemprop.data.splitting.SplitType attribute) (chemprop.data.SplitType attribute) RDKit2DFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.molecule) REAC_DIFF (chemprop.featurizers.molgraph.reaction.RxnMode attribute) (chemprop.featurizers.molgraph.RxnMode attribute) (chemprop.featurizers.RxnMode attribute) REAC_DIFF_BALANCE (chemprop.featurizers.molgraph.reaction.RxnMode attribute) (chemprop.featurizers.molgraph.RxnMode attribute) (chemprop.featurizers.RxnMode attribute) REAC_PROD (chemprop.featurizers.molgraph.reaction.RxnMode attribute) (chemprop.featurizers.molgraph.RxnMode attribute) (chemprop.featurizers.RxnMode attribute) REAC_PROD_BALANCE (chemprop.featurizers.molgraph.reaction.RxnMode attribute) (chemprop.featurizers.molgraph.RxnMode attribute) (chemprop.featurizers.RxnMode attribute) ReactionDatapoint (class in chemprop.data) (class in chemprop.data.datapoints) ReactionDataset (class in chemprop.data) (class in chemprop.data.datasets) register() (chemprop.utils.ClassRegistry method) (chemprop.utils.registry.ClassRegistry method) RegressionCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator)

RegressionConformalCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) RegressionConformalEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) RegressionEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) RegressionFFN (class in chemprop.nn) (class in chemprop.nn.predictors) release (in module conf) RELU (chemprop.nn.Activation attribute) (chemprop.nn.utils.Activation attribute) reset() (chemprop.data.datasets.MoleculeDataset method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.MoleculeDataset method) (chemprop.data.MulticomponentDataset method) rev_edge_index (chemprop.data.BatchMolGraph attribute) (chemprop.data.collate.BatchMolGraph attribute) (chemprop.data.MolGraph attribute) (chemprop.data.molgraph.MolGraph attribute) rg (chemprop.data.ClassBalanceSampler attribute) (chemprop.data.samplers.ClassBalanceSampler attribute) (chemprop.data.samplers.SeededSampler attribute) (chemprop.data.SeededSampler attribute) RMSE (class in chemprop.nn) (class in chemprop.nn.metrics) Rxn (in module chemprop.types) RxnMode (class in chemprop.featurizers) (class in chemprop.featurizers.molgraph) (class in chemprop.featurizers.molgraph.reaction)

S

S (in module chemprop.featurizers) (in module chemprop.featurizers.base) save_model() (in module chemprop.models) (in module chemprop.models.utils) SCAFFOLD_BALANCED (chemprop.data.splitting.SplitType attribute) (chemprop.data.SplitType attribute) ScaleTransform (class in chemprop.nn) (class in chemprop.nn.transforms) SeededSampler (class in chemprop.data) (class in chemprop.data.samplers) SELU (chemprop.nn.Activation attribute) (chemprop.nn.utils.Activation attribute) setup() (chemprop.nn.AtomMessagePassing method) (chemprop.nn.BondMessagePassing method) (chemprop.nn.message_passing.AtomMessagePassing method) (chemprop.nn.message_passing.base.AtomMessagePassing method) (chemprop.nn.message_passing.base.BondMessagePassing method) (chemprop.nn.message_passing.BondMessagePassing method) shape (chemprop.featurizers.base.GraphFeaturizer property) (chemprop.featurizers.GraphFeaturizer property) shared (chemprop.nn.message_passing.multi.MulticomponentMessagePassing attribute) (chemprop.nn.message_passing.MulticomponentMessagePassing attribute) (chemprop.nn.MulticomponentMessagePassing attribute) shuffle (chemprop.data.ClassBalanceSampler attribute) (chemprop.data.samplers.ClassBalanceSampler attribute)

SID (class in chemprop.nn) (class in chemprop.nn.metrics) SimpleMoleculeMolGraphFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.molgraph) (class in chemprop.featurizers.molgraph.molecule) smiles (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.datasets.MulticomponentDataset property) (chemprop.data.datasets.ReactionDataset property) (chemprop.data.MoleculeDataset property) (chemprop.data.MulticomponentDataset property) (chemprop.data.ReactionDataset property) SpearmanEvaluator (class in chemprop.uncertainty) (class in chemprop.uncertainty.evaluator) SpectralFFN (class in chemprop.nn) (class in chemprop.nn.predictors) split_data_by_indices() (in module chemprop.data) (in module chemprop.data.splitting) SplitType (class in chemprop.data) (class in chemprop.data.splitting) stereo (chemprop.featurizers.bond.MultiHotBondFeaturizer attribute) (chemprop.featurizers.MultiHotBondFeaturizer attribute) SumAggregation (class in chemprop.nn) (class in chemprop.nn.agg)

T

T (in module chemprop.featurizers) (in module chemprop.featurizers.base) (in module chemprop.utils.registry) TANH (chemprop.nn.Activation attribute) (chemprop.nn.utils.Activation attribute) task_weights (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.Predictor attribute) templates_path (in module conf) test_step() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) threshold (chemprop.nn.metrics.SID attribute) (chemprop.nn.metrics.Wasserstein attribute) (chemprop.nn.SID attribute) (chemprop.nn.Wasserstein attribute) to() (chemprop.data.BatchMolGraph method) (chemprop.data.collate.BatchMolGraph method) train_step (chemprop.nn.EvidentialFFN attribute) (chemprop.nn.MveFFN attribute) (chemprop.nn.predictors.EvidentialFFN attribute) (chemprop.nn.predictors.MveFFN attribute) (chemprop.nn.predictors.RegressionFFN attribute) (chemprop.nn.predictors.SpectralFFN attribute) (chemprop.nn.QuantileFFN attribute) (chemprop.nn.RegressionFFN attribute) (chemprop.nn.SpectralFFN attribute)

train_step() (chemprop.nn.BinaryClassificationFFN method) (chemprop.nn.BinaryDirichletFFN method) (chemprop.nn.MulticlassClassificationFFN method) (chemprop.nn.Predictor method) (chemprop.nn.predictors.BinaryClassificationFFN method) (chemprop.nn.predictors.BinaryDirichletFFN method) (chemprop.nn.predictors.MulticlassClassificationFFN method) (chemprop.nn.predictors.MulticlassDirichletFFN method) (chemprop.nn.predictors.Predictor method) training_step() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) TrainingBatch (class in chemprop.data) (class in chemprop.data.collate) transform_variance() (chemprop.nn.transforms.UnscaleTransform method) (chemprop.nn.UnscaleTransform method)

U

UncertaintyCalibratorRegistry (in module chemprop.uncertainty) (in module chemprop.uncertainty.calibrator) UncertaintyEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) UncertaintyEstimatorRegistry (in module chemprop.uncertainty) (in module chemprop.uncertainty.estimator) UncertaintyEvaluatorRegistry (in module chemprop.uncertainty) (in module chemprop.uncertainty.evaluator) Unpickler (class in chemprop.utils.v2_0_to_v2_1) UnscaleTransform (class in chemprop.nn) (class in chemprop.nn.transforms)

update() (chemprop.nn.BinaryMCCLoss method) (chemprop.nn.ChempropMetric method) (chemprop.nn.ClassificationMixin method) (chemprop.nn.metrics.BinaryMCCLoss method) (chemprop.nn.metrics.ChempropMetric method) (chemprop.nn.metrics.ClassificationMixin method) (chemprop.nn.metrics.MulticlassMCCLoss method) (chemprop.nn.metrics.R2Score method) (chemprop.nn.MulticlassMCCLoss method) (chemprop.nn.R2Score method)

V

V (chemprop.data.BatchMolGraph attribute) (chemprop.data.collate.BatchMolGraph attribute) (chemprop.data.MolGraph attribute) (chemprop.data.molgraph.MolGraph attribute) V1 (chemprop.featurizers.atom.AtomFeatureMode attribute) (chemprop.featurizers.AtomFeatureMode attribute) v1() (chemprop.featurizers.atom.MultiHotAtomFeaturizer class method) (chemprop.featurizers.MultiHotAtomFeaturizer class method) V1RDKit2DFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.molecule) V1RDKit2DFeaturizerMixin (class in chemprop.featurizers.molecule) V1RDKit2DNormalizedFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.molecule) V2 (chemprop.featurizers.atom.AtomFeatureMode attribute) (chemprop.featurizers.AtomFeatureMode attribute) v2() (chemprop.featurizers.atom.MultiHotAtomFeaturizer class method) (chemprop.featurizers.MultiHotAtomFeaturizer class method) V_d (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.datapoints.MoleculeDatapoint attribute) (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute) (chemprop.data.MoleculeDatapoint attribute) (chemprop.data.TrainingBatch attribute)

V_ds (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.MoleculeDataset property) V_f (chemprop.data.datapoints.MoleculeDatapoint attribute) (chemprop.data.MoleculeDatapoint attribute) V_fs (chemprop.data.datasets.MoleculeDataset property) (chemprop.data.MoleculeDataset property) v_kl (chemprop.nn.DirichletLoss attribute) (chemprop.nn.EvidentialLoss attribute) (chemprop.nn.metrics.DirichletLoss attribute) (chemprop.nn.metrics.EvidentialLoss attribute) V_transform (chemprop.nn.GraphTransform attribute) (chemprop.nn.transforms.GraphTransform attribute) validation_step() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) values() (chemprop.utils.EnumMapping class method) (chemprop.utils.utils.EnumMapping class method) VectorFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.base)

W

w (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.TrainingBatch attribute) W (chemprop.nn.agg.AttentiveAggregation attribute) (chemprop.nn.AttentiveAggregation attribute)

warmup_epochs (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) Wasserstein (class in chemprop.nn) (class in chemprop.nn.metrics) weight (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute)

X

X_d (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) x_d (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute)

X_d (chemprop.data.TrainingBatch attribute) X_d_transform (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute)

Y

Y (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute)

y (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute) Y (chemprop.data.TrainingBatch attribute)

Z

ZelikmanCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator)

ZScalingCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator)