Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Y | Z _ _MetaContainer (class in torchdrug.core) A accuracy() (in module torchdrug.metrics) adjacency (Graph property) aggregate() (ChebyshevConv method) (ContinuousFilterConv method) (GeometricRelationalGraphConv method) (GraphAttentionConv method) (GraphConv method) (GraphIsomorphismConv method) (MessagePassing method) (MessagePassingBase method) (NeuralFingerprintConv method) (RelationalGraphConv method) AlphaCarbonNode (class in torchdrug.layers.geometry) AlphaFoldDB (class in torchdrug.datasets) AnglePrediction (class in torchdrug.tasks) area_under_prc() (in module torchdrug.metrics) area_under_roc() (in module torchdrug.metrics) as_mask() (in module torchdrug.layers.functional) atom() (Molecule method) atom2graph (Molecule property) (PackedMolecule property) atom_center_identification() (in module torchdrug.data.feature) atom_default() (in module torchdrug.data.feature) atom_explicit_property_prediction() (in module torchdrug.data.feature) atom_position() (in module torchdrug.data.feature) atom_pretrain() (in module torchdrug.data.feature) atom_property_prediction() (in module torchdrug.data.feature) atom_reference() (Molecule method) atom_residue_symbol() (in module torchdrug.data.feature) atom_symbol() (in module torchdrug.data.feature) atom_synthon_completion() (in module torchdrug.data.feature) atom_types (MoleculeDataset property) (ReactionDataset property) AttributeMasking (class in torchdrug.tasks) AUPRC() (in module torchdrug.metrics) AUROC() (in module torchdrug.metrics) AutoregressiveGeneration (class in torchdrug.tasks) B BACE (class in torchdrug.datasets) batch_size (Graph property) (PackedGraph property) BBBP (class in torchdrug.datasets) BetaLactamase (class in torchdrug.datasets) BinaryLocalization (class in torchdrug.datasets) BindingDB (class in torchdrug.datasets) bond() (Molecule method) bond2graph (Molecule property) (PackedMolecule property) bond_default() (in module torchdrug.data.feature) bond_length() (in module torchdrug.data.feature) bond_pretrain() (in module torchdrug.data.feature) bond_property_prediction() (in module torchdrug.data.feature) bond_reference() (Molecule method) bond_types (MoleculeDataset property) (ReactionDataset property) BondEdge (class in torchdrug.layers.geometry) C cached_property() (in module torchdrug.utils) capture_rdkit_log() (in module torchdrug.utils) cat() (in module torchdrug.utils) (in module torchdrug.utils.comm) CenterIdentification (class in torchdrug.tasks) CEP (class in torchdrug.datasets) ChebNet (in module torchdrug.models) ChebyshevConv (class in torchdrug.layers) ChebyshevConvolutionalNetwork (class in torchdrug.models) ChEMBLFiltered (class in torchdrug.datasets) chemical_validity() (in module torchdrug.metrics) CiteSeer (class in torchdrug.datasets) ClinTox (class in torchdrug.datasets) clone() (Graph method) (in module torchdrug.utils) (PackedGraph method) (PackedProtein method) combine() (ChebyshevConv method) (ContinuousFilterConv method) (GraphAttentionConv method) (GraphConv method) (GraphIsomorphismConv method) (MessagePassing method) (MessagePassingBase method) (NeuralFingerprintConv method) (RelationalGraphConv method) compact() (Graph method) ComplEx (class in torchdrug.models) complex_score() (in module torchdrug.layers.functional) Compose (class in torchdrug.transforms) compute_md5() (in module torchdrug.utils) ConditionalFlow (class in torchdrug.layers) Configurable (class in torchdrug.core) connected_component_id (PackedProtein property) (Protein property) connected_components() (Graph method) ContactPrediction (class in torchdrug.tasks) context() (_MetaContainer method) ContextPrediction (class in torchdrug.tasks) ContinuousFilterConv (class in torchdrug.layers) copy_() (Graph method) copy_args() (in module torchdrug.utils) Cora (class in torchdrug.datasets) cpu() (Dictionary method) (Graph method) (in module torchdrug.utils) (PackedGraph method) (PackedProtein method) cuda() (Dictionary method) (Graph method) (in module torchdrug.utils) (PackedGraph method) (PackedProtein method) D data_by_meta() (_MetaContainer method) data_dict (_MetaContainer property) DataLoader (class in torchdrug.data) degree_in (Graph property) degree_out (Graph property) Delaney (class in torchdrug.datasets) detach() (Graph method) (in module torchdrug.utils) (PackedGraph method) (PackedProtein method) device (Dictionary property) (Graph property) Dictionary (class in torchdrug.data) DiffPool (class in torchdrug.layers) DihedralPrediction (class in torchdrug.tasks) directed() (Graph method) DistancePrediction (class in torchdrug.tasks) DistMult (class in torchdrug.models) distmult_score() (in module torchdrug.layers.functional) download() (in module torchdrug.utils) E ECFP() (in module torchdrug.data.feature) echarts() (in module torchdrug.utils.plot) edge() (Graph method) edge2graph (Graph property) (PackedGraph property) edge_feature_dim (MoleculeDataset property) (ReactionDataset property) edge_list (Graph property) edge_mask() (Graph method) (Molecule method) (PackedGraph method) (PackedMolecule method) (PackedProtein method) edge_reference() (Graph method) edge_weight (Graph property) EdgePrediction (class in torchdrug.tasks) EdgeSampler (class in torchdrug.layers) Engine (class in torchdrug.core) EnzymeCommission (class in torchdrug.datasets) epoch (Engine property) evaluate() (Engine method) EvolutionaryScaleModeling (class in torchdrug.models) ExtendedConnectivityFingerprint() (in module torchdrug.data.feature) extract() (in module torchdrug.utils) F f1_max() (in module torchdrug.metrics) FB15k (class in torchdrug.datasets) FB15k237 (class in torchdrug.datasets) Fluorescence (class in torchdrug.datasets) Fold (class in torchdrug.datasets) format() (in module torchdrug.utils.pretty) forward() (AlphaCarbonNode method) (AnglePrediction method) (BondEdge method) (ChebyshevConv method) (ChebyshevConvolutionalNetwork method) (ComplEx method) (ConditionalFlow method) (DiffPool method) (DihedralPrediction method) (DistancePrediction method) (DistMult method) (EdgeSampler method) (EvolutionaryScaleModeling method) (GaussianSmearing method) (GeometryAwareRelationalGraphNeuralNetwork method) (GraphAttentionNetwork method) (GraphAutoregressiveFlow method) (GraphConstruction method) (GraphConvolutionalNetwork method) (GraphIsomorphismNetwork method) (IdentityNode method) (IndependentGaussian method) (InfoGraph method) (KNNEdge method) (KnowledgeBaseGraphAttentionNetwork method) (MaxReadout method) (MeanReadout method) (MessagePassingBase method) (MessagePassingNeuralNetwork method) (MinCutPool method) (MultipleBinaryClassification method) (MultiviewContrast method) (NeuralFingerprint method) (NeuralLogicProgramming method) (NodeSampler method) (Physicochemical method) (ProteinBERT method) (ProteinBERTBlock method) (ProteinConvolutionalNetwork method) (ProteinLSTM method) (ProteinResNet method) (ProteinResNetBlock method) (RandomEdgeMask method) (RelationalGraphConvolutionalNetwork method) (RotatE method) (SchNet method) (SelfAttentionBlock method) (SequentialEdge method) (Set2Set method) (SimplE method) (Softmax method) (Sort method) (SpatialEdge method) (SpatialLineGraph method) (Statistic method) (SubsequenceNode method) (SubspaceNode method) (SumReadout method) (TransE method) FreeSolv (class in torchdrug.datasets) from_dense() (Graph class method) from_molecule() (Molecule class method) (PackedMolecule class method) (PackedProtein class method) (Protein class method) from_pdb() (PackedProtein class method) (Protein class method) from_sequence() (PackedProtein class method) (Protein class method) from_smiles() (Molecule class method) (PackedMolecule class method) full() (Graph method) (PackedGraph method) G GAT (in module torchdrug.models) GaussianSmearing (class in torchdrug.layers) GCN (in module torchdrug.models) GCPNGeneration (class in torchdrug.tasks) GearNet (in module torchdrug.models) GeneOntology (class in torchdrug.datasets) generalized_rspmm() (in module torchdrug.layers.functional) generalized_spmm() (in module torchdrug.layers.functional) GeometricRelationalGraphConv (class in torchdrug.layers) GeometryAwareRelationalGraphNeuralNetwork (class in torchdrug.models) get() (Dictionary method) (Registry class method) get_cpu_count() (in module torchdrug.utils.comm) get_edge() (Graph method) get_group() (in module torchdrug.utils.comm) get_item() (PackedGraph method) (PackedProtein method) get_line_count() (in module torchdrug.utils) get_rank() (in module torchdrug.utils.comm) get_world_size() (in module torchdrug.utils.comm) GIN (in module torchdrug.models) Graph (class in torchdrug.data) graph() (Graph method) graph_collate() (in module torchdrug.data) graph_mask() (PackedGraph method) (PackedProtein method) graph_reference() (Graph method) GraphAF (in module torchdrug.models) GraphAttentionConv (class in torchdrug.layers) GraphAttentionNetwork (class in torchdrug.models) GraphAutoregressiveFlow (class in torchdrug.models) GraphConstruction (class in torchdrug.layers.geometry) GraphConv (class in torchdrug.layers) GraphConvolutionalNetwork (class in torchdrug.models) GraphIsomorphismConv (class in torchdrug.layers) GraphIsomorphismNetwork (class in torchdrug.models) H has_key() (Dictionary method) Hetionet (class in torchdrug.datasets) highlight() (in module torchdrug.utils.plot) HIV (class in torchdrug.datasets) HumanPPI (class in torchdrug.datasets) I IdentityNode (class in torchdrug.layers.geometry) IndependentGaussian (class in torchdrug.layers.distribution) InfoGraph (class in torchdrug.models) init_process_group() (in module torchdrug.utils.comm) input_choice() (in module torchdrug.utils) InteractionPrediction (class in torchdrug.tasks) ion_to_molecule() (Molecule method) (PackedMolecule method) is_valid (Molecule property) (PackedMolecule property) K KBGAT (in module torchdrug.models) key_split() (in module torchdrug.data) KNNEdge (class in torchdrug.layers.geometry) KnowledgeBaseGraphAttentionNetwork (class in torchdrug.models) KnowledgeGraphCompletion (class in torchdrug.tasks) KnowledgeGraphDataset (class in torchdrug.data) L ligand_node_feature_dim (ProteinLigandDataset property) line_graph() (Graph method) (PackedGraph method) Lipophilicity (class in torchdrug.datasets) literal_eval() (in module torchdrug.utils) load() (Engine method) load_config_dict() (Engine class method) load_csv() (MoleculeDataset method) load_extension() (in module torchdrug.utils) load_fasta() (ProteinDataset method) load_lmdbs() (ProteinDataset method) (ProteinLigandDataset method) (ProteinPairDataset method) load_pdbs() (ProteinDataset method) load_pickle() (MoleculeDataset method) (ProteinDataset method) load_sequence() (ProteinDataset method) (ProteinLigandDataset method) (ProteinPairDataset method) load_smiles() (MoleculeDataset method) (ReactionDataset method) load_state_dict() (Retrosynthesis method) load_triplet() (KnowledgeGraphDataset method) load_tsv() (KnowledgeGraphDataset method) (NodeClassificationDataset method) load_tsvs() (KnowledgeGraphDataset method) log() (Meter method) log_config() (Meter method) logP() (in module torchdrug.metrics) long_array() (in module torchdrug.utils.pretty) M Malaria (class in torchdrug.datasets) masked_mean() (in module torchdrug.layers.functional) match() (Graph method) matthews_corrcoef() (in module torchdrug.metrics) MaxReadout (class in torchdrug.layers) mean() (in module torchdrug.utils) mean_with_nan() (in module torchdrug.layers.functional) MeanReadout (class in torchdrug.layers) merge() (PackedGraph method) (PackedProtein method) message() (ChebyshevConv method) (ContinuousFilterConv method) (GraphAttentionConv method) (GraphConv method) (GraphIsomorphismConv method) (MessagePassing method) (MessagePassingBase method) (NeuralFingerprintConv method) (RelationalGraphConv method) message_and_aggregate() (ChebyshevConv method) (ContinuousFilterConv method) (GeometricRelationalGraphConv method) (GraphConv method) (GraphIsomorphismConv method) (MessagePassingBase method) (NeuralFingerprintConv method) (RelationalGraphConv method) MessagePassing (class in torchdrug.layers) MessagePassingBase (class in torchdrug.layers) MessagePassingNeuralNetwork (class in torchdrug.models) Meter (class in torchdrug.core) MinCutPool (class in torchdrug.layers) module torchdrug.utils.pretty mol() (Molecule method) mol_reference() (Molecule method) Molecule (class in torchdrug.data) molecule_default() (in module torchdrug.data.feature) MoleculeDataset (class in torchdrug.data) MOSES (class in torchdrug.datasets) MPNN (in module torchdrug.models) multi_slice() (in module torchdrug.layers.functional) multi_slice_mask() (in module torchdrug.layers.functional) MultiLayerPerceptron (class in torchdrug.layers) multinomial() (in module torchdrug.layers.functional) MultipleBinaryClassification (class in torchdrug.tasks) MultiviewContrast (class in torchdrug.models) MutualInformation (class in torchdrug.layers) MUV (class in torchdrug.datasets) N NeuralFingerprint (class in torchdrug.models) NeuralFingerprintConv (class in torchdrug.layers) NeuralLogicProgramming (class in torchdrug.models) NeuralLP (in module torchdrug.models) NFP (in module torchdrug.models) no_rdkit_log() (in module torchdrug.utils) node() (Graph method) node2graph (Graph property) (PackedGraph property) node_feature_dim (MoleculeDataset property) (NodeClassificationDataset property) (ProteinPairDataset property) (ReactionDataset property) node_mask() (Graph method) (Molecule method) (PackedGraph method) (PackedMolecule method) (PackedProtein method) node_reference() (Graph method) NodeClassificationDataset (class in torchdrug.data) NodePropertyPrediction (class in torchdrug.tasks) NodeSampler (class in torchdrug.layers) NormalizeTarget (class in torchdrug.transforms) num_atom_type (MoleculeDataset property) (ReactionDataset property) num_bond_type (MoleculeDataset property) (ReactionDataset property) num_edge (NodeClassificationDataset property) num_entity (KnowledgeGraphDataset property) num_node (NodeClassificationDataset property) num_relation (KnowledgeGraphDataset property) num_triplet (KnowledgeGraphDataset property) O one_hot() (in module torchdrug.layers.functional) OPV (class in torchdrug.datasets) ordered_scaffold_split() (in module torchdrug.data) P pack() (Graph class method) (Protein class method) packed_type (Graph attribute) (Molecule attribute) (Protein attribute) PackedGraph (class in torchdrug.data) PackedMolecule (class in torchdrug.data) PackedProtein (class in torchdrug.data) padded_to_variadic() (in module torchdrug.layers.functional) PairNorm (class in torchdrug.layers) PCQM4M (class in torchdrug.datasets) PDBBind (class in torchdrug.datasets) pearsonr() (in module torchdrug.metrics) penalized_logP() (in module torchdrug.metrics) Physicochemical (class in torchdrug.models) PPIAffinity (class in torchdrug.datasets) predict_synthon() (CenterIdentification method) preprocess() (AutoregressiveGeneration method) (GCPNGeneration method) (InteractionPrediction method) (MultipleBinaryClassification method) (NodePropertyPrediction method) (PropertyPrediction method) print() (in module torchdrug.utils.pretty) PropertyPrediction (class in torchdrug.tasks) Protein (class in torchdrug.data) protein_node_feature_dim (ProteinLigandDataset property) ProteinBERT (class in torchdrug.models) ProteinBERTBlock (class in torchdrug.layers) ProteinConvolutionalNetwork (class in torchdrug.models) ProteinDataset (class in torchdrug.data) ProteinLigandDataset (class in torchdrug.data) ProteinLSTM (class in torchdrug.models) ProteinNet (class in torchdrug.datasets) ProteinPairDataset (class in torchdrug.data) ProteinResNet (class in torchdrug.models) ProteinResNetBlock (class in torchdrug.layers) ProteinView (class in torchdrug.transforms) PubMed (class in torchdrug.datasets) Q QED() (in module torchdrug.metrics) QM8 (class in torchdrug.datasets) QM9 (class in torchdrug.datasets) R r2() (in module torchdrug.metrics) RandomBFSOrder (class in torchdrug.transforms) RandomEdgeMask (class in torchdrug.layers.geometry) reaction() (in module torchdrug.utils.plot) reaction_types (USPTO50k property) ReactionDataset (class in torchdrug.data) reduce() (in module torchdrug.utils.comm) register() (Registry class method) Registry (class in torchdrug.core) RelationalGraphConv (class in torchdrug.layers) RelationalGraphConvolutionalNetwork (class in torchdrug.models) RemapAtomType (class in torchdrug.transforms) repeat() (Graph method) (PackedGraph method) (PackedProtein method) (Protein method) repeat_interleave() (PackedGraph method) (PackedProtein method) residue() (Protein method) residue2atom() (Protein method) residue2graph (PackedProtein property) (Protein property) residue_default() (in module torchdrug.data.feature) residue_feature_dim (ProteinDataset property) (ProteinLigandDataset property) (ProteinPairDataset property) residue_mask() (PackedProtein method) (Protein method) residue_reference() (Protein method) residue_symbol() (in module torchdrug.data.feature) Retrosynthesis (class in torchdrug.tasks) reverse() (ConditionalFlow method) RGCN (in module torchdrug.models) RotatE (class in torchdrug.models) rotate_score() (in module torchdrug.layers.functional) S SA() (in module torchdrug.metrics) sample() (GraphAutoregressiveFlow method) (IndependentGaussian method) save() (Engine method) save_pickle() (MoleculeDataset method) (ProteinDataset method) scaffold_split() (in module torchdrug.data) SchNet (class in torchdrug.models) search() (Registry class method) SecondaryStructure (class in torchdrug.datasets) SelfAttentionBlock (class in torchdrug.layers) SemiSupervised (class in torchdrug.data) semisupervised() (in module torchdrug.data) Sequential (class in torchdrug.layers) SequentialEdge (class in torchdrug.layers.geometry) Set2Set (class in torchdrug.layers) shifted_softplus() (in module torchdrug.layers.functional) Shuffle (class in torchdrug.transforms) SIDER (class in torchdrug.datasets) SimplE (class in torchdrug.models) simple_score() (in module torchdrug.layers.functional) SinusoidalPositionEmbedding (class in torchdrug.layers) Softmax (class in torchdrug.layers) Solubility (class in torchdrug.datasets) Sort (class in torchdrug.layers) sparse_coo_tensor() (in module torchdrug.utils) SpatialEdge (class in torchdrug.layers.geometry) SpatialLineGraph (class in torchdrug.layers.geometry) spearmanr() (in module torchdrug.metrics) split() (Graph method) (Protein method) Stability (class in torchdrug.datasets) stack() (in module torchdrug.utils) (in module torchdrug.utils.comm) Statistic (class in torchdrug.models) step() (Meter method) subbatch() (PackedGraph method) SubcellularLocalization (class in torchdrug.datasets) subgraph() (Graph method) subresidue() (Protein method) SubsequenceNode (class in torchdrug.layers.geometry) SubspaceNode (class in torchdrug.layers.geometry) SumReadout (class in torchdrug.layers) SynthonCompletion (class in torchdrug.tasks) T tasks (MoleculeDataset property) time() (in module torchdrug.utils.pretty) to() (Graph method) to_dict() (Dictionary method) to_molecule() (Molecule method) (PackedMolecule method) (PackedProtein method) (Protein method) to_pdb() (PackedProtein method) (Protein method) to_scaffold() (Molecule method) to_sequence() (PackedProtein method) (Protein method) to_smiles() (Molecule method) (PackedMolecule method) torchdrug.utils.pretty module Tox21 (class in torchdrug.datasets) ToxCast (class in torchdrug.datasets) train() (Engine method) TransE (class in torchdrug.models) transe_score() (in module torchdrug.layers.functional) TruncateProtein (class in torchdrug.transforms) U undirected() (Graph method) (Molecule method) (PackedGraph method) (PackedMolecule method) (PackedProtein method) unpack() (PackedGraph method) unpack_data() (PackedGraph method) unpacked_type (PackedGraph attribute) (PackedMolecule attribute) (PackedProtein attribute) Unsupervised (class in torchdrug.tasks) update() (Meter method) USPTO50k (class in torchdrug.datasets) V variadic_accuracy() (in module torchdrug.metrics) variadic_arange() (in module torchdrug.layers.functional) variadic_area_under_prc() (in module torchdrug.metrics) variadic_area_under_roc() (in module torchdrug.metrics) variadic_cross_entropy() (in module torchdrug.layers.functional) variadic_log_softmax() (in module torchdrug.layers.functional) variadic_max() (in module torchdrug.layers.functional) variadic_mean() (in module torchdrug.layers.functional) variadic_meshgrid() (in module torchdrug.layers.functional) variadic_randperm() (in module torchdrug.layers.functional) variadic_sample() (in module torchdrug.layers.functional) variadic_softmax() (in module torchdrug.layers.functional) variadic_sort() (in module torchdrug.layers.functional) variadic_sum() (in module torchdrug.layers.functional) variadic_to_padded() (in module torchdrug.layers.functional) variadic_top_precision() (in module torchdrug.metrics) variadic_topk() (in module torchdrug.layers.functional) VirtualAtom (class in torchdrug.transforms) VirtualNode (class in torchdrug.transforms) visualize() (Graph method) (Molecule method) (PackedGraph method) (PackedMolecule method) W WN18 (class in torchdrug.datasets) WN18RR (class in torchdrug.datasets) Y YeastPPI (class in torchdrug.datasets) Z ZINC250k (class in torchdrug.datasets) ZINC2m (class in torchdrug.datasets)