todos

[ZiyaoLi]

• 1 MainInferenceLoop Main Inference Loop
• 2 InputFeatureEmbedder Construct an initial single (1D) embedding
• 3 RelativePositionEncoding Relative position encoding
• 4 one_hot One-hot encoding with nearest bin
• 5 AtomAttentionEncoder Atom attention encoder
• 6 AtomAttentionDecoder Atom attention decoder
• 7 AtomTransformer Atom Transformer
• 8 MsaModule MSA Module
• 9 OuterProductMean Outer product mean
• 10 MSAPairWeightedAveraging MSA row-wise gated self-attention using only pair bias
• 11 Transition Transition layer
• 12 TriangleMultiplicationOutgoing Triangular multiplicative update using “outgoing” edges
• 13 TriangleMultiplicationIncoming Triangular multiplicative update using “incoming” edges
• 14 TriangleAttentionStartingNode Triangular gated self-attention around starting node
• 15 TriangleAttentionEndingNode Triangular gated self-attention around ending node
• 16 TemplateEmbedder Template embedder
• 17 PairformerStack Pairformer stack
• 18 SampleDiffusion Sample Diffusion
• 19 CentreRandomAugmentation Centre and Random Augmentation
• 20 DiffusionModule Diffusion Module
• 21 DiffusionConditioning Diffusion Conditioning
• 22 FourierEmbedding Fourier Embedding
• 23 DiffusionTransformer Diffusion Transformer
• 24 AttentionPairBias Attention with pair bias
• 25 ConditionedTransitionBlock Conditioned Transition Block
• 26 AdaLN Adaptive LayerNorm
• 27 SmoothLDDTLoss Smooth LDDT Loss
• 28 weighted_rigid_align Weighted Rigid Align
• 29 expressCoordinatesInFrame Express coordinates in frame
• 30 computeAlignmentError Compute alignment error
• 31 ConfidenceHead Confidence head