Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __call__ (chemprop.utils.ClassRegistry attribute) (chemprop.utils.registry.ClassRegistry attribute) __call__() (chemprop.featurizers.atom.MultiHotAtomFeaturizer method) (chemprop.featurizers.atom.RIGRAtomFeaturizer method) (chemprop.featurizers.base.Featurizer method) (chemprop.featurizers.BinaryFeaturizerMixin method) (chemprop.featurizers.bond.MultiHotBondFeaturizer method) (chemprop.featurizers.bond.RIGRBondFeaturizer method) (chemprop.featurizers.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.CountFeaturizerMixin method) (chemprop.featurizers.CuikmolmakerMolGraphFeaturizer method) (chemprop.featurizers.Featurizer method) (chemprop.featurizers.molecule.BinaryFeaturizerMixin method) (chemprop.featurizers.molecule.ChargeFeaturizer method) (chemprop.featurizers.molecule.CountFeaturizerMixin method) (chemprop.featurizers.molecule.RDKit2DFeaturizer method) (chemprop.featurizers.molecule.V1RDKit2DFeaturizerMixin method) (chemprop.featurizers.molgraph.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer method) (chemprop.featurizers.molgraph.molecule.CuikmolmakerMolGraphFeaturizer 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.CuikmolmakerDataset method) (chemprop.data.datasets.CuikmolmakerDataset method) (chemprop.data.datasets.MolAtomBondDataset method) (chemprop.data.datasets.MoleculeDataset method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.datasets.ReactionDataset method) (chemprop.data.MolAtomBondDataset 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) __getitems__() (chemprop.data.CuikmolmakerDataset method) (chemprop.data.datasets.CuikmolmakerDataset 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.LazyMoleculeDatapoint method) (chemprop.data.datapoints.MoleculeDatapoint method) (chemprop.data.datapoints.ReactionDatapoint method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.LazyMoleculeDatapoint 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.atom.RIGRAtomFeaturizer method) (chemprop.featurizers.BatchCuikMolGraph method) (chemprop.featurizers.bond.MultiHotBondFeaturizer method) (chemprop.featurizers.bond.RIGRBondFeaturizer method) (chemprop.featurizers.molecule.ChargeFeaturizer 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.molecule.BatchCuikMolGraph 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.BatchMolAtomBondGraph method) (chemprop.data.BatchMolGraph method) (chemprop.data.collate.BatchMolAtomBondGraph method) (chemprop.data.collate.BatchMolGraph method) (chemprop.data.datapoints.LazyMoleculeDatapoint method) (chemprop.data.datapoints.MolAtomBondDatapoint 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.LazyMoleculeDatapoint method) (chemprop.data.MolAtomBondDatapoint method) (chemprop.data.MoleculeDatapoint method) (chemprop.data.MoleculeDataset method) (chemprop.data.MulticomponentDataset method) (chemprop.data.ReactionDatapoint method) (chemprop.data.ReactionDataset method) (chemprop.featurizers.BatchCuikMolGraph method) (chemprop.featurizers.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.CuikmolmakerMolGraphFeaturizer method) (chemprop.featurizers.molgraph.CondensedGraphOfReactionFeaturizer method) (chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer method) (chemprop.featurizers.molgraph.molecule.BatchCuikMolGraph method) (chemprop.featurizers.molgraph.molecule.CuikmolmakerMolGraphFeaturizer 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) add_h (chemprop.featurizers.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.molecule.CuikmolmakerMolGraphFeaturizer attribute) agg (chemprop.models.model.MPNN attribute) (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN 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.PointQuantileLoss attribute) (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) atom_constrainer (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) atom_constraint (chemprop.data.datapoints.MolAtomBondDatapoint attribute) (chemprop.data.MolAtomBondDatapoint attribute) atom_constraints (chemprop.data.datasets.MolAtomBondDataset property) (chemprop.data.MolAtomBondDataset property) atom_fdim (chemprop.featurizers.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.molecule.CuikmolmakerMolGraphFeaturizer attribute) atom_featurizer_mode (chemprop.featurizers.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.molecule.CuikmolmakerMolGraphFeaturizer attribute) atom_gt_mask (chemprop.data.datapoints.MolAtomBondDatapoint attribute) (chemprop.data.datasets.MolAtomBondDataset property) (chemprop.data.MolAtomBondDatapoint attribute) (chemprop.data.MolAtomBondDataset property) atom_lt_mask (chemprop.data.datapoints.MolAtomBondDatapoint attribute) (chemprop.data.datasets.MolAtomBondDataset property) (chemprop.data.MolAtomBondDatapoint attribute) (chemprop.data.MolAtomBondDataset property) atom_predictor (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) atom_y (chemprop.data.datapoints.MolAtomBondDatapoint attribute) atom_Y (chemprop.data.datasets.MolAtomBondDataset property) atom_y (chemprop.data.MolAtomBondDatapoint attribute) atom_Y (chemprop.data.MolAtomBondDataset property) AtomFeatureMode (class in chemprop.featurizers) (class in chemprop.featurizers.atom) atomic_nums (chemprop.featurizers.atom.MultiHotAtomFeaturizer attribute) (chemprop.featurizers.atom.RIGRAtomFeaturizer 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) (chemprop.featurizers.BatchCuikMolGraph attribute) (chemprop.featurizers.molgraph.molecule.BatchCuikMolGraph attribute) BatchCuikMolGraph (class in chemprop.featurizers) (class in chemprop.featurizers.molgraph.molecule) BatchMolAtomBondGraph (class in chemprop.data) (class in chemprop.data.collate) BatchMolGraph (class in chemprop.data) (class in chemprop.data.collate) BatchType (in module chemprop.models.model) 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.MolAtomBondTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.datasets.CuikBatchedDatum attribute) (chemprop.data.MolAtomBondTrainingBatch attribute) (chemprop.data.TrainingBatch attribute) bmgs (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.MulticomponentTrainingBatch attribute) bn (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) bns (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) bond_batch (chemprop.data.BatchMolAtomBondGraph attribute) (chemprop.data.collate.BatchMolAtomBondGraph attribute) bond_constrainer (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) bond_constraint (chemprop.data.datapoints.MolAtomBondDatapoint attribute) (chemprop.data.MolAtomBondDatapoint attribute) bond_constraints (chemprop.data.datasets.MolAtomBondDataset property) (chemprop.data.MolAtomBondDataset property) bond_fdim (chemprop.featurizers.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.molecule.CuikmolmakerMolGraphFeaturizer attribute) bond_gt_mask (chemprop.data.datapoints.MolAtomBondDatapoint attribute) (chemprop.data.datasets.MolAtomBondDataset property) (chemprop.data.MolAtomBondDatapoint attribute) (chemprop.data.MolAtomBondDataset property) bond_lt_mask (chemprop.data.datapoints.MolAtomBondDatapoint attribute) (chemprop.data.datasets.MolAtomBondDataset property) (chemprop.data.MolAtomBondDatapoint attribute) (chemprop.data.MolAtomBondDataset property) bond_predictor (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) bond_types (chemprop.featurizers.bond.MultiHotBondFeaturizer attribute) (chemprop.featurizers.MultiHotBondFeaturizer attribute) bond_y (chemprop.data.datapoints.MolAtomBondDatapoint attribute) bond_Y (chemprop.data.datasets.MolAtomBondDataset property) bond_y (chemprop.data.MolAtomBondDatapoint attribute) bond_Y (chemprop.data.MolAtomBondDataset property) 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) ChargeFeaturizer (class in chemprop.featurizers.molecule) 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.mol_atom_bond 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.mixins module chemprop.nn.message_passing.mol_atom_bond 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_cuik_batch() (in module chemprop.data.collate) collate_mol_atom_bond_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.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN method) (chemprop.models.MPNN method) ConstrainerFFN (class in chemprop.nn) (class in chemprop.nn.ffn) constraints (chemprop.data.collate.MolAtomBondTrainingBatch attribute) (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondTrainingBatch attribute) 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_model_file_v2_0_to_v2_1() (in module chemprop.utils.v2_0_to_v2_1) 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) create_and_call_object() (in module chemprop.utils) (in module chemprop.utils.utils) criterion (chemprop.models.model.MPNN property) (chemprop.models.MPNN property) (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.Predictor attribute) criterions (chemprop.models.mol_atom_bond.MolAtomBondMPNN property) (chemprop.models.MolAtomBondMPNN property) CrossEntropyLoss (class in chemprop.nn) (class in chemprop.nn.metrics) CuikBatchedDatum (class in chemprop.data.datasets) CuikmolmakerDataset (class in chemprop.data) (class in chemprop.data.datasets) CuikmolmakerMolGraphFeaturizer (class in chemprop.featurizers) (class in chemprop.featurizers.molgraph) (class in chemprop.featurizers.molgraph.molecule) D d_ed (chemprop.data.datasets.MolAtomBondDataset property) (chemprop.data.MolAtomBondDataset property) 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.CuikmolmakerDataset attribute) (chemprop.data.datasets.CuikmolmakerDataset attribute) (chemprop.data.datasets.MolAtomBondDataset attribute) (chemprop.data.datasets.MoleculeDataset attribute) (chemprop.data.datasets.ReactionDataset attribute) (chemprop.data.MolAtomBondDataset 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.atom.RIGRAtomFeaturizer 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) (chemprop.featurizers.BatchCuikMolGraph attribute) (chemprop.featurizers.molgraph.molecule.BatchCuikMolGraph attribute) E_d (chemprop.data.collate.MolAtomBondTrainingBatch attribute) (chemprop.data.datapoints.MolAtomBondDatapoint attribute) (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondDatapoint attribute) (chemprop.data.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondTrainingBatch attribute) E_ds (chemprop.data.datasets.MolAtomBondDataset property) (chemprop.data.MolAtomBondDataset property) E_f (chemprop.data.datapoints.LazyMoleculeDatapoint attribute) (chemprop.data.datapoints.MoleculeDatapoint attribute) (chemprop.data.LazyMoleculeDatapoint 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) (chemprop.featurizers.BatchCuikMolGraph attribute) (chemprop.featurizers.molgraph.molecule.BatchCuikMolGraph 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.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN 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.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.molecule.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.molecule.SimpleMoleculeMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.SimpleMoleculeMolGraphFeaturizer attribute) (chemprop.featurizers.SimpleMoleculeMolGraphFeaturizer attribute) extra_bond_fdim (chemprop.featurizers.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.CuikmolmakerMolGraphFeaturizer attribute) (chemprop.featurizers.molgraph.molecule.CuikmolmakerMolGraphFeaturizer attribute) (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.NLogProbEnrichment method) (chemprop.nn.metrics.PointQuantileLoss 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.CuikmolmakerDataset attribute) (chemprop.data.datasets.CuikmolmakerDataset attribute) (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 (chemprop.nn.ConstrainerFFN attribute) (chemprop.nn.ffn.ConstrainerFFN attribute) FFN (class in chemprop.nn.ffn) final_lr (chemprop.models.model.MPNN attribute) (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) (chemprop.models.MPNN attribute) find_class() (chemprop.utils.v2_0_to_v2_1.Unpickler method) fingerprint() (chemprop.models.model.MPNN method) (chemprop.models.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN 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.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN 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.ConstrainerFFN method) (chemprop.nn.EvidentialFFN method) (chemprop.nn.ffn.ConstrainerFFN method) (chemprop.nn.ffn.FFN method) (chemprop.nn.GraphTransform method) (chemprop.nn.MABMessagePassing method) (chemprop.nn.MeanAggregation method) (chemprop.nn.message_passing.MABMessagePassing 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.MABMessagePassing 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) from_smi() (chemprop.data.datapoints.MolAtomBondDatapoint class method) (chemprop.data.MolAtomBondDatapoint class method) 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_batch_size() (chemprop.models.model.MPNN method) (chemprop.models.MPNN method) (chemprop.models.multi.MulticomponentMPNN method) (chemprop.models.MulticomponentMPNN method) get_memory_usage() (in module chemprop.utils.utils) get_multi_hot_atom_featurizer() (in module chemprop.featurizers) (in module chemprop.featurizers.atom) get_zstats() (chemprop.nn.metrics.NLogProbEnrichment static method) 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.CuikBatchedDatum attribute) (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute) (chemprop.data.MulticomponentTrainingBatch attribute) (chemprop.data.TrainingBatch attribute) gt_masks (chemprop.data.collate.MolAtomBondTrainingBatch attribute) (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondTrainingBatch attribute) H HasHParams (class in chemprop.nn.hparams) higher_is_better (chemprop.nn.BinaryMCCMetric attribute) (chemprop.nn.ChempropMetric attribute) (chemprop.nn.metrics.BinaryMCCMetric attribute) (chemprop.nn.metrics.ChempropMetric attribute) (chemprop.nn.metrics.MulticlassMCCMetric attribute) (chemprop.nn.MulticlassMCCMetric 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.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) (chemprop.models.MPNN attribute) input_dim (chemprop.nn.ffn.FFN attribute) (chemprop.nn.ffn.MLP property) (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.Predictor attribute) InvalidShapeError is_cuikmolmaker_available() (in module chemprop.utils.utils) 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 LazyMoleculeDatapoint (class in chemprop.data) (class in chemprop.data.datapoints) 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) LIGHTNING_26_COMPAT_ARGS (in module chemprop.conf) load_from_checkpoint() (chemprop.models.model.MPNN class method) (chemprop.models.mol_atom_bond.MolAtomBondMPNN class method) (chemprop.models.MolAtomBondMPNN class method) (chemprop.models.MPNN class method) load_from_file() (chemprop.models.model.MPNN class method) (chemprop.models.mol_atom_bond.MolAtomBondMPNN class method) (chemprop.models.MolAtomBondMPNN 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.datasets) (in module chemprop.data.splitting) (in module chemprop.featurizers.molecule) (in module chemprop.featurizers.molgraph.reaction) (in module chemprop.models.model) (in module chemprop.models.mol_atom_bond) (in module chemprop.models.multi) (in module chemprop.nn.message_passing.multi) (in module chemprop.nn.utils) (in module chemprop.uncertainty.calibrator) (in module chemprop.utils.v1_to_v2) 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.CuikBatchedDatum attribute) (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute) (chemprop.data.MulticomponentTrainingBatch attribute) (chemprop.data.TrainingBatch attribute) lt_masks (chemprop.data.collate.MolAtomBondTrainingBatch attribute) (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondTrainingBatch attribute) M MABAtomMessagePassing (class in chemprop.nn) (class in chemprop.nn.message_passing) (class in chemprop.nn.message_passing.mol_atom_bond) MABBondMessagePassing (class in chemprop.nn) (class in chemprop.nn.message_passing) (class in chemprop.nn.message_passing.mol_atom_bond) MABMessagePassing (class in chemprop.nn) (class in chemprop.nn.message_passing) (class in chemprop.nn.message_passing.proto) 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_encoder_index() (in module chemprop.utils.v1_to_v2) max_lr (chemprop.models.model.MPNN attribute) (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) (chemprop.models.MPNN attribute) MeanAggregation (class in chemprop.nn) (class in chemprop.nn.agg) message_passing (chemprop.models.model.MPNN attribute) (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN 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) method (chemprop.nn.metrics.NLogProbEnrichment attribute) MetricRegistry (in module chemprop.nn) (in module chemprop.nn.metrics) metrics (chemprop.models.model.MPNN attribute) (chemprop.models.MPNN attribute) metricss (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) mg (chemprop.data.datasets.Datum attribute) (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.Datum attribute) (chemprop.data.MolAtomBondDatum 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) 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.mol_atom_bond 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.mixins chemprop.nn.message_passing.mol_atom_bond 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 mol_predictor (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) MolAtomBondDatapoint (class in chemprop.data) (class in chemprop.data.datapoints) MolAtomBondDataset (class in chemprop.data) (class in chemprop.data.datasets) MolAtomBondDatum (class in chemprop.data) (class in chemprop.data.datasets) MolAtomBondGraphDataset (in module chemprop.data.datasets) MolAtomBondMPNN (class in chemprop.models) (class in chemprop.models.mol_atom_bond) MolAtomBondTrainingBatch (class in chemprop.data) (class in chemprop.data.collate) 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) (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 n1 (chemprop.nn.metrics.NLogProbEnrichment attribute) n2 (chemprop.nn.metrics.NLogProbEnrichment attribute) 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_targetss (chemprop.models.mol_atom_bond.MolAtomBondMPNN property) (chemprop.models.MolAtomBondMPNN property) 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) n_taskss (chemprop.models.mol_atom_bond.MolAtomBondMPNN property) (chemprop.models.MolAtomBondMPNN property) n_workers (chemprop.data.datasets.MoleculeDataset attribute) (chemprop.data.datasets.ReactionDataset attribute) (chemprop.data.MoleculeDataset attribute) (chemprop.data.ReactionDataset 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) NLogProbEnrichment (class in chemprop.nn.metrics) 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.MolAtomBondDataset method) (chemprop.data.datasets.MoleculeDataset method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.MolAtomBondDataset method) (chemprop.data.MoleculeDataset method) (chemprop.data.MulticomponentDataset method) normalize_targets() (chemprop.data.datasets.MolAtomBondDataset method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.MolAtomBondDataset method) (chemprop.data.MulticomponentDataset method) NoUncertaintyEstimator (class in chemprop.uncertainty) (class in chemprop.uncertainty.estimator) num_Hs (chemprop.featurizers.atom.MultiHotAtomFeaturizer attribute) (chemprop.featurizers.atom.RIGRAtomFeaturizer attribute) (chemprop.featurizers.MultiHotAtomFeaturizer attribute) num_only() (chemprop.featurizers.atom.MultiHotAtomFeaturizer method) (chemprop.featurizers.atom.RIGRAtomFeaturizer method) (chemprop.featurizers.MultiHotAtomFeaturizer method) O on_validation_model_eval() (chemprop.models.model.MPNN method) (chemprop.models.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN 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.bond.RIGRBondFeaturizer 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_dims (chemprop.nn.MABMessagePassing attribute) (chemprop.nn.message_passing.MABMessagePassing attribute) (chemprop.nn.message_passing.proto.MABMessagePassing attribute) output_dimss (chemprop.models.mol_atom_bond.MolAtomBondMPNN property) (chemprop.models.MolAtomBondMPNN property) output_transform (chemprop.nn.Predictor attribute) (chemprop.nn.predictors.Predictor attribute) P p (chemprop.uncertainty.calibrator.ZelikmanCalibrator attribute) (chemprop.uncertainty.ZelikmanCalibrator attribute) parallel_execute() (in module chemprop.utils) (in module chemprop.utils.utils) PlattCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) PointQuantileLoss (class in chemprop.nn.metrics) pos_idxs (chemprop.data.ClassBalanceSampler attribute) (chemprop.data.samplers.ClassBalanceSampler attribute) predict_step() (chemprop.models.model.MPNN method) (chemprop.models.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN 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) predictors (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) 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.MolAtomBondDataset method) (chemprop.data.datasets.MoleculeDataset method) (chemprop.data.datasets.MulticomponentDataset method) (chemprop.data.MolAtomBondDataset 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) (chemprop.featurizers.BatchCuikMolGraph attribute) (chemprop.featurizers.molgraph.molecule.BatchCuikMolGraph attribute) rg (chemprop.data.ClassBalanceSampler attribute) (chemprop.data.samplers.ClassBalanceSampler attribute) (chemprop.data.samplers.SeededSampler attribute) (chemprop.data.SeededSampler attribute) RIGR (chemprop.featurizers.atom.AtomFeatureMode attribute) (chemprop.featurizers.AtomFeatureMode attribute) RIGRAtomFeaturizer (class in chemprop.featurizers.atom) RIGRBondFeaturizer (class in chemprop.featurizers.bond) 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) setup() (chemprop.nn.AtomMessagePassing method) (chemprop.nn.BondMessagePassing method) (chemprop.nn.MABAtomMessagePassing method) (chemprop.nn.MABBondMessagePassing 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) (chemprop.nn.message_passing.MABAtomMessagePassing method) (chemprop.nn.message_passing.MABBondMessagePassing method) (chemprop.nn.message_passing.mol_atom_bond.MABAtomMessagePassing method) (chemprop.nn.message_passing.mol_atom_bond.MABBondMessagePassing 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.CuikmolmakerDataset property) (chemprop.data.datasets.CuikmolmakerDataset property) (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.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN 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.BatchMolAtomBondGraph method) (chemprop.data.BatchMolGraph method) (chemprop.data.collate.BatchMolAtomBondGraph method) (chemprop.data.collate.BatchMolGraph method) (chemprop.featurizers.BatchCuikMolGraph method) (chemprop.featurizers.molgraph.molecule.BatchCuikMolGraph 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.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN 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) (chemprop.featurizers.BatchCuikMolGraph attribute) (chemprop.featurizers.molgraph.molecule.BatchCuikMolGraph 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.MolAtomBondTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.datapoints.LazyMoleculeDatapoint attribute) (chemprop.data.datapoints.MoleculeDatapoint attribute) (chemprop.data.datasets.CuikBatchedDatum attribute) (chemprop.data.datasets.Datum attribute) (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.Datum attribute) (chemprop.data.LazyMoleculeDatapoint attribute) (chemprop.data.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondTrainingBatch 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) (chemprop.data.MulticomponentTrainingBatch attribute) V_f (chemprop.data.datapoints.LazyMoleculeDatapoint attribute) (chemprop.data.datapoints.MoleculeDatapoint attribute) (chemprop.data.LazyMoleculeDatapoint 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.mol_atom_bond.MolAtomBondMPNN method) (chemprop.models.MolAtomBondMPNN 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.MolAtomBondTrainingBatch attribute) (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.MolAtomBondTrainingBatch attribute) (chemprop.data.MulticomponentTrainingBatch attribute) (chemprop.data.TrainingBatch attribute) W (chemprop.nn.agg.AttentiveAggregation attribute) (chemprop.nn.AttentiveAggregation attribute) warmup_epochs (chemprop.models.model.MPNN attribute) (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) (chemprop.models.MPNN attribute) Wasserstein (class in chemprop.nn) (class in chemprop.nn.metrics) weight (chemprop.data.datasets.Datum attribute) (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.Datum attribute) (chemprop.data.MolAtomBondDatum attribute) weights (chemprop.data.datasets.CuikBatchedDatum attribute) X X_d (chemprop.data.collate.MolAtomBondTrainingBatch attribute) (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.datasets.CuikBatchedDatum attribute) x_d (chemprop.data.datasets.Datum attribute) (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.Datum attribute) (chemprop.data.MolAtomBondDatum attribute) X_d (chemprop.data.MolAtomBondTrainingBatch attribute) (chemprop.data.MulticomponentTrainingBatch attribute) (chemprop.data.TrainingBatch attribute) X_d_transform (chemprop.models.model.MPNN attribute) (chemprop.models.mol_atom_bond.MolAtomBondMPNN attribute) (chemprop.models.MolAtomBondMPNN attribute) (chemprop.models.MPNN attribute) Y Y (chemprop.data.collate.MulticomponentTrainingBatch attribute) (chemprop.data.collate.TrainingBatch attribute) (chemprop.data.datasets.CuikBatchedDatum attribute) y (chemprop.data.datasets.Datum attribute) (chemprop.data.Datum attribute) Y (chemprop.data.MulticomponentTrainingBatch attribute) (chemprop.data.TrainingBatch attribute) Ys (chemprop.data.collate.MolAtomBondTrainingBatch attribute) ys (chemprop.data.datasets.MolAtomBondDatum attribute) (chemprop.data.MolAtomBondDatum attribute) Ys (chemprop.data.MolAtomBondTrainingBatch attribute) Z ZelikmanCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator) zinterval (chemprop.nn.metrics.NLogProbEnrichment attribute) zscale (chemprop.nn.metrics.NLogProbEnrichment attribute) ZScalingCalibrator (class in chemprop.uncertainty) (class in chemprop.uncertainty.calibrator)