Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X _ __call__() (kinoml.features.core.BaseFeaturizer method) (kinoml.ml.lightning_modules.AttrList method) (kinoml.ml.torch_loops.EarlyStopping method) (kinoml.ml.torch_loops.LRScheduler method) __eq__() (kinoml.core.conditions.BaseConditions method) (kinoml.core.measurements.BaseMeasurement method) __getattr__() (kinoml.ml.lightning_modules._IterWithObsModel method) __getitem__() (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.torch_datasets.AwkwardArrayDataset method) (kinoml.datasets.torch_datasets.MultiXTorchDataset method) (kinoml.datasets.torch_datasets.PrefeaturizedTorchDataset method) (kinoml.datasets.torch_datasets.TorchDataset method) (kinoml.datasets.torch_datasets.XyTorchDataset method) (kinoml.datasets.torch_geometric_datasets.AwkwardArrayGeometricDataset method) __getstate__() (kinoml.features.core.ParallelBaseFeaturizer method) __git_revision__ (in module kinoml) __hash__() (kinoml.core.conditions.BaseConditions method) __iter__() (kinoml.datasets.torch_geometric_datasets.AwkwardArrayGeometricDataset method) (kinoml.ml.lightning_modules._IterWithObsModel method) (kinoml.ml.lightning_modules.ObservationModelDataLoader method) __len__() (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.torch_datasets.AwkwardArrayDataset method) (kinoml.datasets.torch_datasets.MultiXTorchDataset method) (kinoml.datasets.torch_datasets.PrefeaturizedTorchDataset method) (kinoml.datasets.torch_datasets.XyTorchDataset method) (kinoml.datasets.torch_geometric_datasets.AwkwardArrayGeometricDataset method) __missing__() (kinoml.utils.defaultdictwithargs method) __next__() (kinoml.ml.lightning_modules._IterWithObsModel method) __repr__() (kinoml.core.components.MolecularComponent method) (kinoml.core.conditions.BaseConditions method) (kinoml.core.measurements.BaseMeasurement method) (kinoml.core.systems.System method) (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) (kinoml.datasets.torch_datasets.AwkwardArrayDataset method) (kinoml.datasets.torch_geometric_datasets.AwkwardArrayGeometricDataset method) (kinoml.features.core.BaseFeaturizer method) __setstate__() (kinoml.features.core.ParallelBaseFeaturizer method) __str__() (kinoml.datasets.torch_datasets.AwkwardArrayDataset method) (kinoml.datasets.torch_geometric_datasets.AwkwardArrayGeometricDataset method) __version__ (in module kinoml) _accessor_to_indices() (in module kinoml.datasets.torch_datasets) _activation (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) _active_dataset_index (kinoml.ml.lightning_modules.MultiDataModule attribute) _add_ligand_entity_info() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer static method) _add_pdb_resolution() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer static method) _assemble_components() (kinoml.features.core.OEBaseModelingFeaturizer method) _BaseModule (class in kinoml.ml.torch_models) _build_dataloader() (kinoml.ml.lightning_modules.MultiDataModule method) _by_fingerprint() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer static method) _by_klifs_sequence() (kinoml.features.complexes.KLIFSConformationTemplatesFeaturizer static method) _by_mcs() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer static method) _by_openeye_shape() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer method) _by_schrodinger_shape() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer method) _check_schrodinger() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer method) _common_validation_test_epoch_end() (kinoml.ml.lightning_modules.ObservationModelModule method) _common_validation_test_step() (kinoml.ml.lightning_modules.ObservationModelModule method) _COMPATIBLE_LIGAND_TYPES (kinoml.features.complexes.SingleLigandProteinComplexFeaturizer attribute) (kinoml.features.ligand.SingleLigandFeaturizer attribute) _COMPATIBLE_PROTEIN_TYPES (kinoml.features.complexes.KLIFSConformationTemplatesFeaturizer attribute) (kinoml.features.complexes.SingleLigandProteinComplexFeaturizer attribute) (kinoml.features.protein.SingleProteinFeaturizer attribute) _components_by_type() (kinoml.core.systems.System method) _connectivity_COO_format() (kinoml.features.ligand.GraphLigandFeaturizer static method) _counter (kinoml.features.protein.AminoAcidCompositionFeaturizer attribute) _create_klifs_structure_db() (kinoml.features.complexes.KLIFSConformationTemplatesFeaturizer method) _data (kinoml.datasets.torch_datasets.MultiXTorchDataset attribute) _dataloaders (kinoml.ml.lightning_modules.CrossValidateTrainer attribute) _default_func() (kinoml.features.core.CallableFeaturizer static method) _disabled_validation_epoch_end() (kinoml.ml.lightning_modules.ObservationModelModule method) _disabled_validation_step() (kinoml.ml.lightning_modules.ObservationModelModule method) _dock_molecule() (kinoml.features.complexes.SCHRODINGERDockingFeaturizer method) _download_to_cache_or_retrieve() (kinoml.datasets.core.DatasetProvider class method) _errors (kinoml.core.measurements.BaseMeasurement attribute) _fast_key_access (kinoml.datasets.torch_datasets.MultiXTorchDataset attribute) _featurize() (kinoml.features.core.BaseFeaturizer method) (kinoml.features.core.Concatenated method) (kinoml.features.core.NullFeaturizer method) (kinoml.features.core.ParallelBaseFeaturizer method) (kinoml.features.core.Pipeline method) (kinoml.features.core.TupleOfArrays method) _featurize_one() (kinoml.features.complexes.KLIFSConformationTemplatesFeaturizer method) (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer method) (kinoml.features.complexes.OEComplexFeaturizer method) (kinoml.features.complexes.OEDockingFeaturizer method) (kinoml.features.complexes.SCHRODINGERComplexFeaturizer method) (kinoml.features.complexes.SCHRODINGERDockingFeaturizer method) (kinoml.features.core.BaseFeaturizer method) (kinoml.features.core.BaseOneHotEncodingFeaturizer method) (kinoml.features.core.CallableFeaturizer method) (kinoml.features.core.ClearFeaturizations method) (kinoml.features.core.HashFeaturizer method) (kinoml.features.core.PadFeaturizer method) (kinoml.features.ligand.GraphLigandFeaturizer method) (kinoml.features.ligand.MorganFingerprintFeaturizer method) (kinoml.features.protein.AminoAcidCompositionFeaturizer method) (kinoml.features.protein.OEProteinStructureFeaturizer method) _filter_structures() (kinoml.features.complexes.KLIFSConformationTemplatesFeaturizer static method) _from_dispatcher() (kinoml.utils.FromDistpatcherMixin class method) _get_array() (kinoml.features.core.PadFeaturizer method) _get_components() (kinoml.features.core.OEBaseModelingFeaturizer static method) _get_design_unit() (kinoml.features.core.OEBaseModelingFeaturizer method) _get_most_similar_klifs_ligand_entity() (kinoml.features.complexes.KLIFSConformationTemplatesFeaturizer method) _get_most_similar_pdb_ligand_entity() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer method) _get_pdb_ligand_entities() (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer method) _get_protein_residue_numbers() (kinoml.features.core.OEBaseModelingFeaturizer static method) _getitem_multi_X() (kinoml.datasets.torch_datasets.MultiXTorchDataset method) _getitem_single_X() (kinoml.datasets.torch_datasets.MultiXTorchDataset method) _getter() (kinoml.features.core.HashFeaturizer static method) _hybridization_names (kinoml.features.ligand.GraphLigandFeaturizer attribute) _is_npz (kinoml.datasets.torch_datasets.MultiXTorchDataset attribute) _IterWithObsModel (class in kinoml.ml.lightning_modules) _key_to_ints() (kinoml.datasets.torch_datasets.MultiXTorchDataset static method) _kinase_klifs_sequence (kinoml.core.proteins.KLIFSKinase attribute) _loss_adapter_generic() (kinoml.core.measurements.ObservationModelMeasurement static method) _loss_adapter_pytorch() (kinoml.core.measurements.ObservationModelMeasurement class method) _loss_adapter_xgboost_mse() (kinoml.core.measurements.PercentageDisplacementMeasurement static method) (kinoml.core.measurements.pIC50Measurement static method) (kinoml.core.measurements.pKdMeasurement static method) (kinoml.core.measurements.pKiMeasurement static method) _models (kinoml.ml.lightning_modules.CrossValidateTrainer attribute) _molecule (kinoml.core.ligands.Ligand attribute) (kinoml.core.proteins.Protein attribute) _observation_model() (kinoml.core.measurements.ObservationModelMeasurement class method) _observation_model_null() (kinoml.core.measurements.ObservationModelMeasurement static method) _observation_model_numpy (kinoml.core.measurements.pIC50Measurement attribute) (kinoml.core.measurements.pKdMeasurement attribute) (kinoml.core.measurements.pKiMeasurement attribute) _observation_model_numpy() (kinoml.core.measurements.PercentageDisplacementMeasurement static method) _observation_model_pytorch() (kinoml.core.measurements.ObservationModelMeasurement static method) (kinoml.core.measurements.PercentageDisplacementMeasurement static method) (kinoml.core.measurements.pIC50Measurement static method) (kinoml.core.measurements.pKdMeasurement static method) (kinoml.core.measurements.pKiMeasurement static method) _observation_model_xgboost (kinoml.core.measurements.PercentageDisplacementMeasurement attribute) (kinoml.core.measurements.pIC50Measurement attribute) (kinoml.core.measurements.pKdMeasurement attribute) (kinoml.core.measurements.pKiMeasurement attribute) _observation_model_xgboost() (kinoml.core.measurements.ObservationModelMeasurement static method) _old_training_loop() (in module kinoml.ml.torch_loops) _patch_paths_for_kfold() (kinoml.ml.lightning_modules.CrossValidateTrainer method) _pdb_id (kinoml.core.proteins.Protein attribute) _per_atom_features() (kinoml.features.ligand.GraphLigandFeaturizer method) _pH (kinoml.core.conditions.AssayConditions attribute) _post_featurize() (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) (kinoml.features.complexes.KLIFSConformationTemplatesFeaturizer method) (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer method) (kinoml.features.core.BaseFeaturizer method) (kinoml.features.core.ClearFeaturizations method) _post_loss_adapter() (kinoml.core.measurements.ObservationModelMeasurement static method) (kinoml.core.measurements.PercentageDisplacementMeasurement static method) (kinoml.core.measurements.pIC50Measurement static method) (kinoml.core.measurements.pKdMeasurement static method) (kinoml.core.measurements.pKiMeasurement static method) _postprocess_structure() (kinoml.features.complexes.SCHRODINGERComplexFeaturizer static method) _pre_featurize() (kinoml.features.complexes.KLIFSConformationTemplatesFeaturizer method) (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer method) (kinoml.features.complexes.SCHRODINGERComplexFeaturizer method) (kinoml.features.core.BaseFeaturizer method) (kinoml.features.core.PadFeaturizer method) _prepare_structure() (kinoml.features.complexes.SCHRODINGERComplexFeaturizer method) _preprocess_structure() (kinoml.features.complexes.SCHRODINGERComplexFeaturizer method) _process_protein() (kinoml.features.core.OEBaseModelingFeaturizer method) _properties() (kinoml.core.conditions.BaseConditions method) _query_klifs() (kinoml.core.proteins.KLIFSKinase method) _query_ncbi() (kinoml.core.sequences.AminoAcidSequence method) _query_sequence_sources() (kinoml.core.proteins.KLIFSKinase method) (kinoml.core.sequences.AminoAcidSequence method) (kinoml.core.sequences.Biosequence method) _query_uniprot() (kinoml.core.sequences.AminoAcidSequence method) _raw_data (kinoml.datasets.core.DatasetProvider attribute) _read_protein_structure() (kinoml.features.complexes.SCHRODINGERComplexFeaturizer method) (kinoml.features.core.OEBaseModelingFeaturizer method) _remove_clashing_water() (kinoml.features.core.OEBaseModelingFeaturizer static method) _replace_ligand() (kinoml.features.complexes.SCHRODINGERDockingFeaturizer static method) _retrieve_sequence() (kinoml.features.core.BaseOneHotEncodingFeaturizer method) (kinoml.features.ligand.OneHotSMILESFeaturizer method) (kinoml.features.protein.OneHotEncodedSequenceFeaturizer method) _sequence (kinoml.core.sequences.Biosequence attribute) _shape_X() (kinoml.datasets.torch_datasets.MultiXTorchDataset method) _shortname (kinoml.features.core.Pipeline attribute) _smiles (kinoml.core.ligands.Ligand attribute) _standard_step() (kinoml.ml.lightning_modules.ObservationModelModule method) _store_docking_score() (kinoml.features.complexes.OEDockingFeaturizer static method) (kinoml.features.complexes.SCHRODINGERDockingFeaturizer static method) _str_keys_to_nested_dict() (kinoml.datasets.torch_datasets.MultiXTorchDataset method) _structure_klifs_residues (kinoml.core.proteins.KLIFSKinase attribute) _structure_klifs_sequence (kinoml.core.proteins.KLIFSKinase attribute) _SUPPORTED_SIMILARITY_METRICS (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer attribute) _SUPPORTED_TYPES (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer attribute) (kinoml.features.complexes.OEComplexFeaturizer attribute) (kinoml.features.complexes.OEDockingFeaturizer attribute) (kinoml.features.complexes.SCHRODINGERComplexFeaturizer attribute) (kinoml.features.complexes.SCHRODINGERDockingFeaturizer attribute) (kinoml.features.core.BaseFeaturizer attribute) (kinoml.features.core.ParallelBaseFeaturizer attribute) _supports() (kinoml.features.complexes.SingleLigandProteinComplexFeaturizer method) (kinoml.features.core.BaseFeaturizer method) (kinoml.features.ligand.SingleLigandFeaturizer method) (kinoml.features.protein.SingleProteinFeaturizer method) _system_to_name() (kinoml.features.complexes.SCHRODINGERComplexFeaturizer static method) _to_dataset() (kinoml.datasets.core.DatasetProvider method) _trainers (kinoml.ml.lightning_modules.CrossValidateTrainer attribute) _update_pdb_header() (kinoml.features.core.OEBaseModelingFeaturizer method) _values (kinoml.core.measurements.BaseMeasurement attribute) _write_complex_mae() (kinoml.features.complexes.SCHRODINGERDockingFeaturizer method) _write_results() (kinoml.features.core.OEBaseModelingFeaturizer method) A active_dataset (kinoml.ml.lightning_modules.MultiDataModule property) active_dataset_index (kinoml.ml.lightning_modules.MultiDataModule property) ALL_ATOMIC_SYMBOLS (kinoml.features.ligand.GraphLigandFeaturizer attribute) ALPHABET (kinoml.core.sequences.AminoAcidSequence attribute) (kinoml.core.sequences.Biosequence attribute) (kinoml.core.sequences.DNASequence attribute) (kinoml.core.sequences.RNASequence attribute) (kinoml.features.core.BaseOneHotEncodingFeaturizer attribute) (kinoml.features.ligand.OneHotSMILESFeaturizer attribute), [1] (kinoml.features.protein.OneHotEncodedSequenceFeaturizer attribute) AminoAcidCompositionFeaturizer (class in kinoml.features.protein) AminoAcidSequence (class in kinoml.core.sequences) APPDIR (in module kinoml.utils) apply_deletions() (in module kinoml.modeling.OEModeling) apply_insertions() (in module kinoml.modeling.OEModeling) apply_mutations() (in module kinoml.modeling.OEModeling) are_identical_molecules() (in module kinoml.modeling.OEModeling) as_dataloader() (kinoml.datasets.torch_datasets.PrefeaturizedTorchDataset method) AssayConditions (class in kinoml.core.conditions) assign() (kinoml.datasets.groups.BaseGrouper method) assign_caps() (in module kinoml.modeling.OEModeling) AttrList (class in kinoml.ml.lightning_modules) AwkwardArrayDataset (class in kinoml.datasets.torch_datasets) AwkwardArrayGeometricDataset (class in kinoml.datasets.torch_geometric_datasets) axis (kinoml.features.core.Concatenated attribute) B BaseConditions (class in kinoml.core.conditions) BaseDatasetProvider (class in kinoml.datasets.core) BaseFeaturizer (class in kinoml.features.core) BaseFilter (class in kinoml.datasets.groups) BaseGrouper (class in kinoml.datasets.groups) BaseLigand (class in kinoml.core.components) BaseMeasurement (class in kinoml.core.measurements) BaseOneHotEncodingFeaturizer (class in kinoml.features.core) BaseProtein (class in kinoml.core.components) best_loss (kinoml.ml.torch_loops.EarlyStopping attribute) best_run() (kinoml.ml.lightning_modules.CrossValidateTrainer method) Biosequence (class in kinoml.core.sequences) build_loops (kinoml.features.complexes.SCHRODINGERComplexFeaturizer attribute) C cache_dir (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer attribute) (kinoml.features.complexes.SCHRODINGERComplexFeaturizer attribute) (kinoml.features.core.OEBaseModelingFeaturizer attribute) call (kinoml.utils.defaultdictwithargs attribute) callable (kinoml.features.core.CallableFeaturizer attribute) CallableFeaturizer (class in kinoml.features.core) CallableGrouper (class in kinoml.datasets.groups) check() (kinoml.core.conditions.AssayConditions method) (kinoml.core.conditions.BaseConditions method) (kinoml.core.measurements.BaseMeasurement method) (kinoml.core.measurements.PercentageDisplacementMeasurement method) (kinoml.core.measurements.pIC50Measurement method) (kinoml.core.measurements.pKdMeasurement method) (kinoml.core.measurements.pKiMeasurement method) (kinoml.core.systems.LigandSystem method) (kinoml.core.systems.ProteinLigandComplex method) (kinoml.core.systems.ProteinSystem method) (kinoml.core.systems.System method) ChEMBLDatasetProvider (class in kinoml.datasets.chembl) chunksize (kinoml.features.core.ParallelBaseFeaturizer attribute) clear() (kinoml.ml.lightning_modules.CrossValidateTrainer method) ClearFeaturizations (class in kinoml.features.core) CNN() (in module kinoml.ml.tensorflow_models) collapsible() (in module kinoml.utils) components (kinoml.core.systems.System attribute) compute() (kinoml.ml.lightning_modules.RootMeanSquaredError method) Concatenated (class in kinoml.features.core) conditions (kinoml.core.measurements.BaseMeasurement attribute) (kinoml.datasets.core.BaseDatasetProvider property) (kinoml.datasets.core.DatasetProvider property) configure_optimizers() (kinoml.ml.lightning_modules.ObservationModelModule method) convolution (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) convolution_ligand (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) convolution_protein (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) ConvolutionNeuralNetworkRegression (class in kinoml.ml.torch_models) ConvolutionNeuralNetworkRegressionProteinInformed (class in kinoml.ml.torch_models) counter (kinoml.ml.torch_loops.EarlyStopping attribute) CrossValidateTrainer (class in kinoml.ml.lightning_modules) D dask_client (kinoml.features.core.ParallelBaseFeaturizer attribute) data (kinoml.datasets.torch_datasets.AwkwardArrayDataset attribute) (kinoml.datasets.torch_geometric_datasets.AwkwardArrayGeometricDataset attribute) data_X (kinoml.datasets.torch_datasets.XyTorchDataset attribute) data_y (kinoml.datasets.torch_datasets.MultiXTorchDataset attribute) (kinoml.datasets.torch_datasets.XyTorchDataset attribute) dataloader_options (kinoml.ml.lightning_modules.MultiDataModule attribute) datapath() (in module kinoml.utils) dataset_indices_by_size() (kinoml.ml.lightning_modules.MultiDataModule method) dataset_map (kinoml.ml.lightning_modules.MultiDataModule attribute) DatasetProvider (class in kinoml.datasets.core) datasets (kinoml.ml.lightning_modules.MultiDataModule attribute) defaultdictwithargs (class in kinoml.utils) delete() (kinoml.core.sequences.Biosequence method) delete_alterations() (in module kinoml.modeling.MDAnalysisModeling) delete_clashing_sidechains() (in module kinoml.modeling.OEModeling) delete_expression_tags() (in module kinoml.modeling.MDAnalysisModeling) delete_incomplete_backbone_residues() (in module kinoml.modeling.MDAnalysisModeling) delete_partial_residues() (in module kinoml.modeling.OEModeling) delete_residue() (in module kinoml.modeling.OEModeling) delete_residues() (in module kinoml.modeling.MDAnalysisModeling) delete_short_protein_segments() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) denominator (kinoml.features.core.HashFeaturizer attribute) DenseNeuralNetworkRegression (class in kinoml.ml.torch_models) device (kinoml.datasets.torch_datasets.PrefeaturizedTorchDataset attribute) dictionary (kinoml.features.core.BaseOneHotEncodingFeaturizer attribute) DIRECTORY (kinoml.utils.FileDownloader attribute) (kinoml.utils.LocalFileStorage attribute) DNASequence (class in kinoml.core.sequences) DNN() (in module kinoml.ml.tensorflow_models) download_fasta_file() (in module kinoml.databases.uniprot) download_file() (in module kinoml.utils) download_pdb_ligand() (in module kinoml.databases.pdb) download_pdb_structure() (in module kinoml.databases.pdb) dropout (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) dropout_percentage (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) E early_stop (kinoml.ml.torch_loops.EarlyStopping attribute) EarlyStopping (class in kinoml.ml.torch_loops) embedding_shape (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) embedding_shape_ligand (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) embedding_shape_protein (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) enumerate_isomeric_smiles() (in module kinoml.modeling.OEModeling) errors (kinoml.core.measurements.BaseMeasurement property) estimate_input_shape() (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork static method) (kinoml.ml.torch_models._BaseModule static method) (kinoml.ml.torch_models.ListOfTupleNeuralNetworkregression static method) estimate_input_size() (kinoml.datasets.torch_datasets.PrefeaturizedTorchDataset method) (kinoml.datasets.torch_datasets.TorchDataset method) F factor (kinoml.ml.torch_loops.LRScheduler attribute) featurizations (kinoml.core.systems.System attribute), [1] featurize() (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) (kinoml.features.core.BaseFeaturizer method) featurized_systems() (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) featurizer (kinoml.datasets.torch_datasets.TorchDataset attribute) featurizer_result() (kinoml.utils.LocalFileStorage static method) featurizers (kinoml.features.core.Pipeline attribute) FileDownloader (class in kinoml.utils) fill_until_next_multiple() (in module kinoml.utils) fit() (kinoml.ml.lightning_modules.CrossValidateTrainer method) forward() (kinoml.ml.lightning_modules.ObservationModelModule method) (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork method) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression method) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed method) (kinoml.ml.torch_models.DenseNeuralNetworkRegression method) (kinoml.ml.torch_models.ListOfTupleNeuralNetworkregression method) (kinoml.ml.torch_models.NeuralNetworkRegression method) (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed method) fred_docking() (in module kinoml.docking.OEDocking) from_file() (kinoml.core.ligands.Ligand class method) (kinoml.core.proteins.Protein class method) from_npz() (kinoml.datasets.torch_datasets.MultiXTorchDataset class method) (kinoml.datasets.torch_datasets.XyTorchDataset class method) from_parquet() (kinoml.datasets.torch_datasets.AwkwardArrayDataset class method) (kinoml.datasets.torch_geometric_datasets.AwkwardArrayGeometricDataset class method) from_pdb() (kinoml.core.proteins.Protein class method) from_smiles() (kinoml.core.ligands.Ligand class method) from_source() (kinoml.datasets.chembl.ChEMBLDatasetProvider class method) (kinoml.datasets.core.BaseDatasetProvider class method) (kinoml.datasets.core.DatasetProvider class method) (kinoml.datasets.pkis2.PKIS2DatasetProvider class method) FromDistpatcherMixin (class in kinoml.utils) fully_connected_1 (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) fully_connected_2 (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) fully_connected_3 (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) fully_connected_4 (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) fully_connected_5 (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) fully_connected_ligand (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) fully_connected_out (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) fully_connected_protein (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) function (kinoml.datasets.groups.CallableGrouper attribute) G generate_conformations() (in module kinoml.modeling.OEModeling) generate_enantiomers() (in module kinoml.modeling.OEModeling) generate_reasonable_conformations() (in module kinoml.modeling.OEModeling) generate_tautomers() (in module kinoml.modeling.OEModeling) get_atom_coordinates() (in module kinoml.modeling.OEModeling) get_expression_tags() (in module kinoml.modeling.OEModeling) get_kfold() (kinoml.ml.lightning_modules.MultiDataModule method) get_sequence() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) get_structure_sequence_alignment() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) getter (kinoml.features.core.HashFeaturizer attribute) GraphConvLayer1 (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) GraphConvLayer2 (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) GraphConvolutionNeuralNetwork (class in kinoml.ml.torch_geometric_models) GraphLigandFeaturizer (class in kinoml.features.ligand) group (kinoml.core.measurements.BaseMeasurement attribute) grouper() (in module kinoml.utils) H HashFeaturizer (class in kinoml.features.core) hidden_shape (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) hybrid_docking() (in module kinoml.docking.OEDocking) I import_object() (in module kinoml.utils) indices (kinoml.datasets.torch_datasets.MultiXTorchDataset attribute) (kinoml.datasets.torch_datasets.XyTorchDataset attribute) indices() (kinoml.datasets.groups.BaseGrouper method) (kinoml.datasets.groups.CallableGrouper method) (kinoml.datasets.groups.RandomGrouper method) indices_by_provider() (kinoml.datasets.core.MultiDatasetProvider method) input_shape (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) input_size() (kinoml.datasets.torch_datasets.XyTorchDataset method) insert() (kinoml.core.sequences.Biosequence method) is_single_X() (kinoml.datasets.torch_datasets.MultiXTorchDataset method) iterator (kinoml.ml.lightning_modules._IterWithObsModel attribute) K kernel_shape (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) key (kinoml.features.core.PadFeaturizer attribute) keys (kinoml.features.core.ClearFeaturizations attribute) KFold3Way (class in kinoml.ml.lightning_modules) kinase_klifs_id (kinoml.core.proteins.KLIFSKinase attribute) kinase_klifs_sequence (kinoml.core.proteins.KLIFSKinase property) kinoml module kinoml.analysis module kinoml.analysis.metrics module kinoml.analysis.plots module kinoml.core module kinoml.core.components module kinoml.core.conditions module kinoml.core.ligands module kinoml.core.measurements module kinoml.core.proteins module kinoml.core.sequences module kinoml.core.systems module kinoml.databases module kinoml.databases.klifs module kinoml.databases.pdb module kinoml.databases.uniprot module kinoml.datasets module kinoml.datasets.chembl module kinoml.datasets.core module kinoml.datasets.groups module kinoml.datasets.pkis2 module kinoml.datasets.torch_datasets module kinoml.datasets.torch_geometric_datasets module kinoml.docking module kinoml.docking.OEDocking module kinoml.docking.SCHRODINGERDocking module kinoml.features module kinoml.features.complexes module kinoml.features.core module kinoml.features.ligand module kinoml.features.protein module kinoml.ml module kinoml.ml.lightning_modules module kinoml.ml.tensorflow_models module kinoml.ml.torch_geometric_models module kinoml.ml.torch_loops module kinoml.ml.torch_models module kinoml.ml.torch_trees module kinoml.modeling module kinoml.modeling.alignment module kinoml.modeling.MDAnalysisModeling module kinoml.modeling.OEModeling module kinoml.modeling.SCHRODINGERModeling module kinoml.optimize module kinoml.utils module kinoml.workflows module klifs_kinase_db() (kinoml.utils.LocalFileStorage static method) klifs_kinase_from_uniprot_id() (in module kinoml.databases.klifs) klifs_ligand_mol2() (kinoml.utils.LocalFileStorage static method) klifs_structure_db() (kinoml.utils.LocalFileStorage static method) KLIFSConformationTemplatesFeaturizer (class in kinoml.features.complexes) KLIFSKinase (class in kinoml.core.proteins) L length_sequence (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) Ligand (class in kinoml.core.ligands) ligand (kinoml.core.systems.LigandSystem property) ligand_protein (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) ligands (kinoml.core.systems.LigandSystem property) LigandSystem (class in kinoml.core.systems) linear (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) ListOfTupleNeuralNetworkregression (class in kinoml.ml.torch_models) LN10 (in module kinoml.core.measurements) LocalFileStorage (class in kinoml.utils) logger (in module kinoml.core.ligands) (in module kinoml.core.proteins) (in module kinoml.core.sequences) (in module kinoml.databases.pdb) (in module kinoml.datasets.chembl) (in module kinoml.datasets.core) (in module kinoml.datasets.pkis2) (in module kinoml.docking.SCHRODINGERDocking) (in module kinoml.features.complexes) (in module kinoml.features.core) (in module kinoml.features.protein) (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) (in module kinoml.modeling.SCHRODINGERModeling) loop_db (kinoml.features.core.OEBaseModelingFeaturizer attribute) loss_adapter() (kinoml.core.measurements.ObservationModelMeasurement class method) (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) loss_adapters() (kinoml.datasets.core.MultiDatasetProvider method) loss_function (kinoml.ml.lightning_modules.ObservationModelModule attribute) lr_scheduler (kinoml.ml.torch_loops.LRScheduler attribute) LRScheduler (class in kinoml.ml.torch_loops) M mae_to_pdb() (in module kinoml.modeling.SCHRODINGERModeling) max_in_ring_size (kinoml.features.ligand.GraphLigandFeaturizer attribute) max_retry (kinoml.features.complexes.SCHRODINGERComplexFeaturizer attribute) measurement_type (kinoml.datasets.core.BaseDatasetProvider property) (kinoml.datasets.core.DatasetProvider property) measurement_types (kinoml.ml.lightning_modules.MultiDataModule attribute) measurements (kinoml.datasets.core.DatasetProvider attribute) (kinoml.datasets.core.MultiDatasetProvider property) (kinoml.datasets.torch_datasets.PrefeaturizedTorchDataset attribute) measurements_as_array() (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) measurements_by_group() (kinoml.datasets.core.BaseDatasetProvider method) metadata (kinoml.core.components.MolecularComponent attribute) (kinoml.core.measurements.BaseMeasurement attribute) (kinoml.core.sequences.Biosequence attribute) (kinoml.datasets.core.DatasetProvider attribute) (kinoml.datasets.core.MultiDatasetProvider attribute) method (kinoml.features.complexes.OEDockingFeaturizer attribute) metric_mae (kinoml.ml.lightning_modules.ObservationModelModule attribute) metric_mse (kinoml.ml.lightning_modules.ObservationModelModule attribute) metric_r2 (kinoml.ml.lightning_modules.ObservationModelModule attribute) metric_rmse (kinoml.ml.lightning_modules.ObservationModelModule attribute) min_delta (kinoml.ml.torch_loops.EarlyStopping attribute) min_lr (kinoml.ml.torch_loops.LRScheduler attribute) module kinoml kinoml.analysis kinoml.analysis.metrics kinoml.analysis.plots kinoml.core kinoml.core.components kinoml.core.conditions kinoml.core.ligands kinoml.core.measurements kinoml.core.proteins kinoml.core.sequences kinoml.core.systems kinoml.databases kinoml.databases.klifs kinoml.databases.pdb kinoml.databases.uniprot kinoml.datasets kinoml.datasets.chembl kinoml.datasets.core kinoml.datasets.groups kinoml.datasets.pkis2 kinoml.datasets.torch_datasets kinoml.datasets.torch_geometric_datasets kinoml.docking kinoml.docking.OEDocking kinoml.docking.SCHRODINGERDocking kinoml.features kinoml.features.complexes kinoml.features.core kinoml.features.ligand kinoml.features.protein kinoml.ml kinoml.ml.lightning_modules kinoml.ml.tensorflow_models kinoml.ml.torch_geometric_models kinoml.ml.torch_loops kinoml.ml.torch_models kinoml.ml.torch_trees kinoml.modeling kinoml.modeling.alignment kinoml.modeling.MDAnalysisModeling kinoml.modeling.OEModeling kinoml.modeling.SCHRODINGERModeling kinoml.optimize kinoml.utils kinoml.workflows MolecularComponent (class in kinoml.core.components) molecule (kinoml.core.ligands.Ligand property) (kinoml.core.proteins.Protein property) MorganFingerprintFeaturizer (class in kinoml.features.ligand) MostSimilarPDBLigandFeaturizer (class in kinoml.features.complexes) MPNN() (in module kinoml.ml.tensorflow_models) multi_measurement_training_loop() (in module kinoml.ml.torch_loops) MultiDataModule (class in kinoml.ml.lightning_modules) MultiDatasetProvider (class in kinoml.datasets.core) MultiXTorchDataset (class in kinoml.datasets.torch_datasets) N n_processes (kinoml.features.core.ParallelBaseFeaturizer attribute) name (kinoml.core.components.MolecularComponent attribute) (kinoml.core.sequences.Biosequence attribute) (kinoml.core.systems.System property) (kinoml.features.core.BaseFeaturizer property) (kinoml.features.core.Pipeline property) nb_character (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) nbits (kinoml.features.ligand.MorganFingerprintFeaturizer attribute) ncbi_id (kinoml.core.sequences.AminoAcidSequence attribute) ncbi_to_uniprot() (kinoml.core.sequences.AminoAcidSequence static method) needs_input_shape (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) (kinoml.ml.torch_models._BaseModule attribute) NeuralNetworkRegression (class in kinoml.ml.torch_models) NeuralNetworkRegressionProteinInformed (class in kinoml.ml.torch_models) nfolds (kinoml.ml.lightning_modules.CrossValidateTrainer attribute) nn_model (kinoml.ml.lightning_modules.ObservationModelModule attribute) normalize (kinoml.features.core.HashFeaturizer attribute) null_observation_model() (in module kinoml.core.measurements) NullFeaturizer (class in kinoml.features.core) O observation_model (kinoml.datasets.torch_datasets.PrefeaturizedTorchDataset attribute) (kinoml.ml.lightning_modules._IterWithObsModel attribute) (kinoml.ml.lightning_modules.ObservationModelDataLoader attribute) observation_model() (kinoml.core.measurements.ObservationModelMeasurement class method) (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) observation_model_map (kinoml.ml.lightning_modules.MultiDataModule attribute) observation_models (kinoml.ml.lightning_modules.MultiDataModule attribute) observation_models() (kinoml.datasets.core.MultiDatasetProvider method) ObservationModelDataLoader (class in kinoml.ml.lightning_modules) ObservationModelMeasurement (class in kinoml.core.measurements) ObservationModelModule (class in kinoml.ml.lightning_modules) OEBaseModelingFeaturizer (class in kinoml.features.core) OEComplexFeaturizer (class in kinoml.features.complexes) OEDockingFeaturizer (class in kinoml.features.complexes) OEProteinStructureFeaturizer (class in kinoml.features.protein) one_hot_encode() (kinoml.features.core.BaseOneHotEncodingFeaturizer static method) OneHotEncodedSequenceFeaturizer (class in kinoml.features.protein) OneHotSMILESFeaturizer (class in kinoml.features.ligand) optimizer (kinoml.ml.lightning_modules.ObservationModelModule attribute) (kinoml.ml.torch_loops.LRScheduler attribute) output_dir (kinoml.features.complexes.SCHRODINGERComplexFeaturizer attribute) (kinoml.features.core.OEBaseModelingFeaturizer attribute) output_shape (kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) (kinoml.ml.torch_models.DenseNeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegression attribute) (kinoml.ml.torch_models.NeuralNetworkRegressionProteinInformed attribute) overlay_molecules() (in module kinoml.modeling.OEModeling) P PACKAGE_ROOT (in module kinoml.utils) pad_with (kinoml.features.core.PadFeaturizer attribute) PadFeaturizer (class in kinoml.features.core) ParallelBaseFeaturizer (class in kinoml.features.core) patience (kinoml.ml.torch_loops.EarlyStopping attribute) (kinoml.ml.torch_loops.LRScheduler attribute) pdb_id (kinoml.core.proteins.Protein property) pdb_smiles_json() (kinoml.utils.LocalFileStorage static method) PercentageDisplacementMeasurement (class in kinoml.core.measurements) performance() (in module kinoml.analysis.metrics) pH (kinoml.core.conditions.AssayConditions property) pIC50Measurement (class in kinoml.core.measurements) Pipeline (class in kinoml.features.core) pKa_norm (kinoml.features.complexes.OEDockingFeaturizer attribute) pKdMeasurement (class in kinoml.core.measurements) pKiMeasurement (class in kinoml.core.measurements) PKIS2DatasetProvider (class in kinoml.datasets.pkis2) pose_molecules() (in module kinoml.docking.OEDocking) predicted_vs_observed() (in module kinoml.analysis.plots) PrefeaturizedTorchDataset (class in kinoml.datasets.torch_datasets) prepare_complex() (in module kinoml.modeling.OEModeling) prepare_protein() (in module kinoml.modeling.OEModeling) prepare_structure() (in module kinoml.modeling.OEModeling) Protein (class in kinoml.core.proteins) protein (kinoml.core.systems.ProteinSystem property) ProteinLigandComplex (class in kinoml.core.systems) proteins (kinoml.core.systems.ProteinSystem property) ProteinSystem (class in kinoml.core.systems) providers (kinoml.datasets.core.MultiDatasetProvider attribute) R radius (kinoml.features.ligand.MorganFingerprintFeaturizer attribute) RandomGrouper (class in kinoml.datasets.groups) RANGE (kinoml.core.measurements.BaseMeasurement attribute), [1] (kinoml.core.measurements.PercentageDisplacementMeasurement attribute) (kinoml.core.measurements.pIC50Measurement attribute) (kinoml.core.measurements.pKdMeasurement attribute) (kinoml.core.measurements.pKiMeasurement attribute) ratios (kinoml.datasets.groups.RandomGrouper attribute) rcsb_electron_density_mtz() (kinoml.utils.FileDownloader static method) (kinoml.utils.LocalFileStorage static method) rcsb_ligand_sdf() (kinoml.utils.LocalFileStorage static method) rcsb_structure_cif() (kinoml.utils.FileDownloader static method) (kinoml.utils.LocalFileStorage static method) rcsb_structure_pdb() (kinoml.utils.FileDownloader static method) (kinoml.utils.LocalFileStorage static method) read_electron_density() (in module kinoml.modeling.OEModeling) read_molecule() (in module kinoml.modeling.MDAnalysisModeling) read_molecules() (in module kinoml.modeling.OEModeling) read_smiles() (in module kinoml.modeling.OEModeling) remove_non_protein() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) renumber_protein_residues() (in module kinoml.modeling.MDAnalysisModeling) renumber_structure() (in module kinoml.modeling.OEModeling) resids_to_box_molecule() (in module kinoml.docking.OEDocking) residue_ids_to_residue_names() (in module kinoml.modeling.OEModeling) RNASequence (class in kinoml.core.sequences) root_mean_squared_error() (in module kinoml.analysis.metrics) RootMeanSquaredError (class in kinoml.ml.lightning_modules) run_docking() (in module kinoml.docking.OEDocking) run_glide() (in module kinoml.docking.SCHRODINGERDocking) run_prepwizard() (in module kinoml.modeling.SCHRODINGERModeling) S SCHRODINGERComplexFeaturizer (class in kinoml.features.complexes) SCHRODINGERDockingFeaturizer (class in kinoml.features.complexes) seed_everything() (in module kinoml.utils) select_altloc() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) select_chain() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) sequence (kinoml.core.sequences.Biosequence property) sequence_similarity() (in module kinoml.modeling.alignment) sequence_type (kinoml.features.protein.OneHotEncodedSequenceFeaturizer attribute) sha256_objects() (in module kinoml.utils) shape (kinoml.features.core.PadFeaturizer attribute) shape_restrain (kinoml.features.complexes.SCHRODINGERDockingFeaturizer attribute) shape_screen() (in module kinoml.modeling.SCHRODINGERModeling) shape_X (kinoml.datasets.torch_datasets.MultiXTorchDataset attribute) shape_y (kinoml.datasets.torch_datasets.MultiXTorchDataset attribute) shortname (kinoml.features.core.Pipeline property) shuffle (kinoml.ml.lightning_modules.CrossValidateTrainer attribute) similarity_metric (kinoml.features.complexes.MostSimilarPDBLigandFeaturizer attribute) SingleLigandFeaturizer (class in kinoml.features.ligand) SingleLigandProteinComplexFeaturizer (class in kinoml.features.complexes) SingleProteinFeaturizer (class in kinoml.features.protein) smiles_from_pdb() (in module kinoml.databases.pdb) smiles_type (kinoml.features.ligand.OneHotSMILESFeaturizer attribute) split() (kinoml.ml.lightning_modules.KFold3Way method) split_by_groups() (kinoml.datasets.core.DatasetProvider method) split_molecule_components() (in module kinoml.modeling.OEModeling) structure_klifs_id (kinoml.core.proteins.KLIFSKinase attribute) structure_klifs_residues (kinoml.core.proteins.KLIFSKinase property) structure_klifs_sequence (kinoml.core.proteins.KLIFSKinase property) style (kinoml.features.core.ClearFeaturizations attribute) substitute() (kinoml.core.sequences.Biosequence method) superpose_proteins() (in module kinoml.modeling.OEModeling) supports() (kinoml.features.core.BaseFeaturizer method) (kinoml.features.core.Pipeline method) System (class in kinoml.core.systems) system (kinoml.core.measurements.BaseMeasurement attribute) systems (kinoml.datasets.core.BaseDatasetProvider property) (kinoml.datasets.core.DatasetProvider property) (kinoml.datasets.torch_datasets.PrefeaturizedTorchDataset attribute) T temp (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegression attribute) temp_ligand (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) temp_protein (kinoml.ml.torch_models.ConvolutionNeuralNetworkRegressionProteinInformed attribute) test() (kinoml.ml.lightning_modules.CrossValidateTrainer method) test_dataloader() (kinoml.ml.lightning_modules.MultiDataModule method) test_epoch_end() (kinoml.ml.lightning_modules.ObservationModelModule method) test_step() (kinoml.ml.lightning_modules.ObservationModelModule method) to_awkward() (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) to_dataframe() (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) to_dict_of_arrays() (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) to_numpy() (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) to_pytorch() (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) to_tensorflow() (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) to_xgboost() (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) toolkit (kinoml.core.proteins.Protein attribute) TorchDataset (class in kinoml.datasets.torch_datasets) train_dataloader() (kinoml.ml.lightning_modules.MultiDataModule method) trainer_args (kinoml.ml.lightning_modules.CrossValidateTrainer attribute) trainer_kwargs (kinoml.ml.lightning_modules.CrossValidateTrainer attribute) training_step() (kinoml.ml.lightning_modules.ObservationModelModule method) TupleOfArrays (class in kinoml.features.core) U uniprot_id (kinoml.core.sequences.AminoAcidSequence attribute) update_residue_identifiers() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) use_multiprocessing (kinoml.features.core.ParallelBaseFeaturizer attribute) V val_dataloader() (kinoml.ml.lightning_modules.MultiDataModule method) validate (kinoml.ml.lightning_modules.ObservationModelModule attribute) values (kinoml.core.measurements.BaseMeasurement property) versions (in module kinoml) W watermark() (in module kinoml.utils) weight (kinoml.core.systems.System property) with_validation (kinoml.ml.lightning_modules.CrossValidateTrainer attribute) write_molecule() (in module kinoml.modeling.MDAnalysisModeling) write_molecules() (in module kinoml.modeling.OEModeling) X XyTorchDataset (class in kinoml.datasets.torch_datasets)