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StructureTokenEncoder

ferritin_plms::esm3::models::vqvae

Struct StructureTokenEncoder 

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pub struct StructureTokenEncoder { /* private fields */ }
Expand description

Encodes backbone coordinates into discrete structure tokens via a 2-layer geometric mini-transformer followed by nearest-neighbour VQ codebook lookup.

Weight layout (in encoder checkpoint):

  • encoder.blocks.* — transformer
  • pre_vq_proj.weight — (d_codebook, enc_d_model)
  • codebook.embeddings— (n_codes, d_codebook)

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impl StructureTokenEncoder

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pub fn load(vb: VarBuilder<'_>, config: VqVaeConfig) -> Result<Self>

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pub fn encode( &self, coords: &Tensor, sequence_id: Option<&Tensor>, chain_id: Option<&Tensor>, ) -> Result<Tensor>

Encode backbone coordinates into structure tokens.

  • coords: (B, L, 3, 3) backbone (N, CA, C) positions.
  • sequence_id: optional (B, L) bin-packing IDs.
  • chain_id: optional (B, L) chain IDs.

Returns (B, L) u32 structure token indices.

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