Struct ESM2Runner 

pub struct ESM2Runner { /* private fields */ }

Implementations

impl ESM2Runner

pub fn load_model(modeltype: ESM2Models, device: Device) -> Result<ESM2Runner>

Load model from HuggingFace hub, downloading config.json, tokenizer files, and weights.

pub fn run_forward(&self, prot_sequence: &str) -> Result<ESM2Output>

pub fn predict_contacts(&self, prot_sequence: &str) -> Result<Tensor>

Predict residue-residue contact probabilities for a single protein sequence.

Returns a (seq_len, seq_len) contact probability matrix (BOS/EOS stripped, so dimensions equal the number of amino acids in prot_sequence).

pub fn decode_logits(&self, output: ESM2Output) -> Result<String>

pub fn get_pseudo_probabilities( &self, prot_sequence: &str, ) -> Result<Vec<PseudoProbability>>

Run ESM2 and return per-residue pseudo-probabilities for the 20 standard amino acids.

BOS and EOS tokens are stripped before softmax is applied. Only amino acid / position pairs with probability > 0.01 are included in the result.

Trait Implementations

impl PlmRunner for ESM2Runner

fn embed(&self, sequence: &str) -> Result<Tensor>

Run the ESM2 transformer and return per-residue embeddings (pre-LM-head).

Shape: (1, L, hidden_size) where L includes BOS and EOS tokens.

fn model_name(&self) -> &str

Model name / identifier string (e.g. “esm2”, “amplify”, “esmc”).