Documentation

• torchdrug.core
  • Configurable
  • Engine
  • Meter
  • Registry
  • Meta Container
• torchdrug.data
  • Data Structures
    • Graph
    • Molecule
    • Protein
    • PackedGraph
    • PackedMolecule
    • PackedProtein
    • Dictionary
  • Datasets
    • KnowledgeGraphDataset
    • MoleculeDataset
    • ProteinDataset
    • ProteinPairDataset
    • ProteinLigandDataset
    • NodeClassificationDataset
    • ReactionDataset
    • SemiSupervised
  • Data Processing
    • DataLoader
    • Dataset Split Methods
  • Feature Functions
    • Atom Features
    • Bond Features
    • Residue Features
    • Molecule Features
  • Element Constants
• torchdrug.datasets
  • Knowledge Graph Datasets
    • FB15k
    • FB15k237
    • WN18
    • WN18RR
    • Hetionet
  • Molecule Property Prediction Datasets
    • BACE
    • BBBP
    • CEP
    • ChEMBLFiltered
    • ClinTox
    • Delaney
    • FreeSolv
    • HIV
    • Lipophilicity
    • MUV
    • Malaria
    • OPV
    • QM8
    • QM9
    • SIDER
    • Tox21
    • ToxCast
    • ZINC250k
    • ZINC2m
    • MOSES
    • PCQM4M
  • Protein Property Prediction Datasets
    • BetaLactamase
    • Fluorescence
    • Stability
    • Solubility
    • BinaryLocalization
    • SubcellularLocalization
    • EnzymeCommission
    • GeneOntology
    • AlphaFoldDB
  • Protein Structure Prediction Datasets
    • Fold
    • SecondaryStructure
    • ProteinNet
  • Protein-Protein Prediction Datasets
    • HumanPPI
    • YeastPPI
    • PPIAffinity
  • Protein Ligand Prediction Datasets
    • BindingDB
    • PDBBind
  • Retrosynthesis Datasets
    • USPTO50k
  • Citation Network Datasets
    • Cora
    • CiteSeer
    • PubMed
• torchdrug.transforms
  • Graph Transformations
    • NormalizeTarget
    • RandomBFSOrder
    • Shuffle
    • VirtualNode
  • Molecule Transformations
    • RemapAtomType
    • VirtualAtom
  • Protein Transformations
    • TruncateProtein
    • ProteinView
• torchdrug.metrics
  • Basic Metrics
    • AUROC
    • AUPRC
    • R2
    • Accuracy
    • Matthews Correlation Coefficient
    • Pearson Correlation Coefficient
    • Spearman’s Rank Correlation Coefficient
    • Variadic Accuracy
    • Variadic Area Under ROC
    • Variadic Area Under PRC
    • Variadic Top Precision
    • F1 Max
  • Chemical Metrics
    • SA
    • QED
    • Chemical Validity
    • LogP
    • Penalized LogP
• torchdrug.layers
  • Common Layers
    • GaussianSmearing
    • MultiLayerPerceptron
    • MutualInformation
    • SinusoidalPositionEmbedding
    • PairNorm
    • Sequential
  • Convolution Layers
    • ChebyshevConv
    • ContinuousFilterConv
    • GeometricRelationalGraphConv
    • GraphAttentionConv
    • GraphConv
    • GraphIsomorphismConv
    • MessagePassing
    • NeuralFingerprintConv
    • RelationalGraphConv
  • Readout Layers
    • MeanReadout
    • SumReadout
    • MaxReadout
    • Set2Set
    • Softmax
    • Sort
  • Pooling Layers
    • DiffPool
    • MinCutPool
  • Sampler Layers
    • EdgeSampler
    • NodeSampler
  • Flow Layers
    • ConditionalFlow
  • Sequence Encoder Blocks
    • ProteinResNetBlock
    • SelfAttentionBlock
    • ProteinBERTBlock
  • Distribution Layers
    • IndependentGaussian
  • Graph Construction Layers
    • GraphConstruction
    • SpatialLineGraph
    • BondEdge
    • KNNEdge
    • SpatialEdge
    • SequentialEdge
    • AlphaCarbonNode
    • IdentityNode
    • RandomEdgeMask
    • SubsequenceNode
    • SubspaceNode
  • Functional Layers
    • Embedding Score Functions
    • Sparse Matrix Multiplication
    • Variadic
    • Tensor Reduction
    • Tensor Construction
    • Sampling
    • Activation
• torchdrug.models
  • Knowledge Graph Reasoning Models
    • TransE
    • DistMult
    • ComplEx
    • SimplE
    • RotatE
    • NeuralLP
    • KBGAT
  • Graph Neural Networks
    • ChebNet
    • GCN
    • GAT
    • GIN
    • MPNN
    • NFP
    • RGCN
    • GearNet
    • SchNet
  • Protein Sequence Encoders
    • ESM
    • ProteinCNN
    • ProteinResNet
    • ProteinLSTM
    • ProteinBERT
    • Statistic Feature Engineering
    • Physicochemical Feature Engineering
  • Normalizing Flows
    • GraphAutoregressiveFlow
  • Self-supervised Models
    • InfoGraph
    • MultiviewContrast
• torchdrug.tasks
  • Property Prediction Tasks
    • PropertyPrediction
    • MultipleBinaryClassification
    • NodePropertyPrediction
    • InteractionPrediction
  • Pre-trained Molecular Representation Tasks
    • EdgePrediction
    • AttributeMasking
    • ContextPrediction
    • DistancePrediction
    • AnglePrediction
    • DihedralPrediction
    • Unsupervised
  • Molecule Generation Tasks
    • AutoregressiveGeneration
    • GCPNGeneration
  • Retrosynthesis Tasks
    • CenterIdentification
    • SynthonCompletion
    • Retrosynthesis
  • Knowledge Graph Reasoning Tasks
    • KnowledgeGraphCompletion
  • Protein-Protein Interaction Prediction Tasks
    • ContactPrediction
• torchdrug.utils
  • Visualization
  • Auxiliary Torch Functions
  • Distributed Communication
  • File Processing
  • Commandline I/O
  • Decorator
  • Helper functions