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) _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) _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) _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) _IterWithObsModel (class in kinoml.ml.lightning_modules) _key_to_ints() (kinoml.datasets.torch_datasets.MultiXTorchDataset static method) _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) _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) _per_atom_features() (kinoml.features.ligand.GraphLigandFeaturizer method) _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) _shape_X() (kinoml.datasets.torch_datasets.MultiXTorchDataset method) _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) _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) _update_pdb_header() (kinoml.features.core.OEBaseModelingFeaturizer method) _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) 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_run() (kinoml.ml.lightning_modules.CrossValidateTrainer method) Biosequence (class in kinoml.core.sequences) C 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) 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) compute() (kinoml.ml.lightning_modules.RootMeanSquaredError method) Concatenated (class in kinoml.features.core) conditions (kinoml.datasets.core.BaseDatasetProvider property) (kinoml.datasets.core.DatasetProvider property) configure_optimizers() (kinoml.ml.lightning_modules.ObservationModelModule method) ConvolutionNeuralNetworkRegression (class in kinoml.ml.torch_models) ConvolutionNeuralNetworkRegressionProteinInformed (class in kinoml.ml.torch_models) CrossValidateTrainer (class in kinoml.ml.lightning_modules) D datapath() (in module kinoml.utils) dataset_indices_by_size() (kinoml.ml.lightning_modules.MultiDataModule method) DatasetProvider (class in kinoml.datasets.core) 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) DenseNeuralNetworkRegression (class in kinoml.ml.torch_models) 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) E EarlyStopping (class in kinoml.ml.torch_loops) 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 featurizations (kinoml.core.systems.System attribute) 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_result() (kinoml.utils.LocalFileStorage static method) 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) 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_config() (in module kinoml._version) get_expression_tags() (in module kinoml.modeling.OEModeling) get_keywords() (in module kinoml._version) 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) get_versions() (in module kinoml) (in module kinoml._version) git_get_keywords() (in module kinoml._version) git_pieces_from_vcs() (in module kinoml._version) git_versions_from_keywords() (in module kinoml._version) GraphConvolutionNeuralNetwork (class in kinoml.ml.torch_geometric_models) GraphLigandFeaturizer (class in kinoml.features.ligand) grouper() (in module kinoml.utils) H HANDLERS (in module kinoml._version) HashFeaturizer (class in kinoml.features.core) hybrid_docking() (in module kinoml.docking.OEDocking) I import_object() (in module kinoml.utils) 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_size() (kinoml.datasets.torch_datasets.XyTorchDataset method) insert() (kinoml.core.sequences.Biosequence method) is_single_X() (kinoml.datasets.torch_datasets.MultiXTorchDataset method) K KFold3Way (class in kinoml.ml.lightning_modules) kinase_klifs_sequence (kinoml.core.proteins.KLIFSKinase property) kinase_klifs_sequence() (kinoml.core.proteins.KLIFSKinase method) kinoml module kinoml._version 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 Ligand (class in kinoml.core.ligands) ligand (kinoml.core.systems.LigandSystem property) ligands (kinoml.core.systems.LigandSystem property) LigandSystem (class in kinoml.core.systems) 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) LONG_VERSION_PY (in module kinoml._version) 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) LRScheduler (class in kinoml.ml.torch_loops) M mae_to_pdb() (in module kinoml.modeling.SCHRODINGERModeling) measurement_type (kinoml.datasets.core.BaseDatasetProvider property) (kinoml.datasets.core.DatasetProvider property) measurements (kinoml.datasets.core.MultiDatasetProvider property) measurements_as_array() (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) measurements_by_group() (kinoml.datasets.core.BaseDatasetProvider method) module kinoml kinoml._version 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) molecule() (kinoml.core.ligands.Ligand method) (kinoml.core.proteins.Protein method) 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 name (kinoml.core.systems.System property) (kinoml.features.core.BaseFeaturizer property) (kinoml.features.core.Pipeline property) 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) NotThisMethod null_observation_model() (in module kinoml.core.measurements) NullFeaturizer (class in kinoml.features.core) O observation_model() (kinoml.core.measurements.ObservationModelMeasurement class method) (kinoml.datasets.core.BaseDatasetProvider method) (kinoml.datasets.core.DatasetProvider method) (kinoml.datasets.core.MultiDatasetProvider method) 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) overlay_molecules() (in module kinoml.modeling.OEModeling) P PACKAGE_ROOT (in module kinoml.utils) PadFeaturizer (class in kinoml.features.core) ParallelBaseFeaturizer (class in kinoml.features.core) 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) pKdMeasurement (class in kinoml.core.measurements) pKiMeasurement (class in kinoml.core.measurements) PKIS2DatasetProvider (class in kinoml.datasets.pkis2) plus_or_dot() (in module kinoml._version) 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) R 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) 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) register_vcs_handler() (in module kinoml._version) remove_non_protein() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) render() (in module kinoml._version) render_git_describe() (in module kinoml._version) render_git_describe_long() (in module kinoml._version) render_pep440() (in module kinoml._version) render_pep440_old() (in module kinoml._version) render_pep440_post() (in module kinoml._version) render_pep440_pre() (in module kinoml._version) 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_command() (in module kinoml._version) 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() (kinoml.core.sequences.Biosequence method) sequence_similarity() (in module kinoml.modeling.alignment) sha256_objects() (in module kinoml.utils) shape_screen() (in module kinoml.modeling.SCHRODINGERModeling) shortname (kinoml.features.core.Pipeline property) 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) 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_residues (kinoml.core.proteins.KLIFSKinase property) structure_klifs_residues() (kinoml.core.proteins.KLIFSKinase method) structure_klifs_sequence (kinoml.core.proteins.KLIFSKinase property) structure_klifs_sequence() (kinoml.core.proteins.KLIFSKinase method) 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) systems (kinoml.datasets.core.BaseDatasetProvider property) (kinoml.datasets.core.DatasetProvider property) T 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) TorchDataset (class in kinoml.datasets.torch_datasets) train_dataloader() (kinoml.ml.lightning_modules.MultiDataModule method) training_step() (kinoml.ml.lightning_modules.ObservationModelModule method) TupleOfArrays (class in kinoml.features.core) U update_residue_identifiers() (in module kinoml.modeling.MDAnalysisModeling) (in module kinoml.modeling.OEModeling) V val_dataloader() (kinoml.ml.lightning_modules.MultiDataModule method) values (kinoml.core.measurements.BaseMeasurement property) VersioneerConfig (class in kinoml._version) versions (in module kinoml) versions_from_parentdir() (in module kinoml._version) W watermark() (in module kinoml.utils) weight (kinoml.core.systems.System property) write_molecule() (in module kinoml.modeling.MDAnalysisModeling) write_molecules() (in module kinoml.modeling.OEModeling) X XyTorchDataset (class in kinoml.datasets.torch_datasets)