List of all items

Structs

• amplify::amplify::AMPLIFY
• amplify::amplify::EncoderBlock
• amplify::amplify::ModelOutput
• amplify::amplify_runner::AmplifyRunner
• amplify::config::AMPLIFYConfig
• esm2::esm2::ESM2
• esm2::esm2::ESM2Attention
• esm2::esm2::ESM2Config
• esm2::esm2::ESM2ContactHead
• esm2::esm2::ESM2Embeddings
• esm2::esm2::ESM2LMHead
• esm2::esm2::ESM2Layer
• esm2::esm2::ESM2Output
• esm2::esm2_runner::ESM2Runner
• esm::layers::attention::MultiHeadAttention
• esm::layers::blocks::SwiGLU
• esm::layers::blocks::UnifiedTransformerBlock
• esm::layers::geom_attention::GeometricReasoningOriginalImpl
• esm::layers::regression_head::RegressionHead
• esm::layers::rotary::RotaryEmbedding
• esm::layers::transformer_stack::TransformerStack
• esm::models::esmc::ESMC
• esm::models::esmc::ESMCConfig
• esm::tokenization::TokenizerCollection
• esm::tokenization::sequence_tokenizer::EsmSequenceTokenizer
• featurize::utilities::AAAtomIter
• ligandmpnn::configs::AABiasConfig
• ligandmpnn::configs::LigandMPNNConfig
• ligandmpnn::configs::MPNNExecConfig
• ligandmpnn::configs::MembraneMPNNConfig
• ligandmpnn::configs::MultiPDBConfig
• ligandmpnn::configs::ProteinMPNNConfig
• ligandmpnn::configs::ResidueControl
• ligandmpnn::configs::RunConfig
• ligandmpnn::model::DecLayer
• ligandmpnn::model::EncLayer
• ligandmpnn::model::ProteinMPNN
• ligandmpnn::model::ScoreOutput
• ligandmpnn::proteinfeatures::ProteinFeatures
• types::ContactMap
• types::PseudoProbability

Enums

• amplify::amplify_runner::AmplifyModels
• esm2::esm2_runner::ESM2Models
• esm::models::esmc::ESMTokenizer
• esm::models::esmc::FfnType
• featurize::utilities::AAAtom
• featurize::utilities::Residue
• ligandmpnn::configs::ModelTypes

Traits

• esm::tokenization::sequence_tokenizer::EsmTokenizerBase
• featurize::StructureFeatures

Functions

• amplify::amplify::apply_rotary_emb
• amplify::amplify::precompute_freqs_cis
• device
• esm::tokenization::get_model_tokenizers
• esm::utils::constants::models::model_is_locally_supported
• esm::utils::constants::models::normalize_model_name
• featurize::utilities::aa1to_int
• featurize::utilities::aa3to1
• featurize::utilities::calculate_cb
• featurize::utilities::cat_neighbors_nodes
• featurize::utilities::compute_nearest_neighbors
• featurize::utilities::create_backbone_mask_37
• featurize::utilities::cross_product
• featurize::utilities::gather_edges
• featurize::utilities::gather_nodes
• featurize::utilities::gather_nodes_t
• featurize::utilities::get_nearest_neighbours
• featurize::utilities::int_to_aa1
• featurize::utilities::linspace
• featurize::utilities::linspace_f32
• featurize::utilities::topk_last_dim
• ligandmpnn::model::multinomial_sample

Constants

• esm::utils::constants::SQRT_3
• esm::utils::constants::esm3::SEQUENCE_VOCAB
• esm::utils::constants::models::ESM3_FUNCTION_DECODER_V0
• esm::utils::constants::models::ESM3_OPEN_SMALL
• esm::utils::constants::models::ESM3_OPEN_SMALL_ALIAS_1
• esm::utils::constants::models::ESM3_OPEN_SMALL_ALIAS_2
• esm::utils::constants::models::ESM3_OPEN_SMALL_ALIAS_3
• esm::utils::constants::models::ESM3_STRUCTURE_DECODER_V0
• esm::utils::constants::models::ESM3_STRUCTURE_ENCODER_V0
• esm::utils::constants::models::ESMC_300M
• esm::utils::constants::models::ESMC_600M