Struct StructureEncoderRunner 

pub struct StructureEncoderRunner { /* private fields */ }

Wraps the ESM3 structure token encoder for converting backbone coordinates to tokens.

Uses a separate checkpoint (data/weights/esm3_structure_encoder_v0.pth) from the main model.

Implementations

impl StructureEncoderRunner

pub fn from_pretrained(device: Device) -> Result<Self>

Load the VQ-VAE structure encoder (ferritin-100.22).

This used to refuse: the port targeted a network the released checkpoint does not contain. All of those differences are now modelled — the stack roots at transformer, its blocks are geometric-only with no attn and no trailing norm, pre_vq_proj carries its bias, and the relative position embedding is loaded and used as the encoder’s initial hidden state.

pub fn from_pretrained_with(opts: &LoadOptions) -> Result<Self>

Load with an explicit device and dtype.

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

Encode backbone coordinates to structure tokens.

• coords: (B, L, 3, 3) backbone (N, CA, C) atom positions.

Returns (B, L) u32 structure token indices.