List of all items

Structs

• amplify::amplify::AMPLIFY
• amplify::amplify::AmplifyOutput
• amplify::amplify::EncoderBlock
• 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
• esm2::saprot_tokenizer::SaProtTokenizer
• esm3::layers::blocks::SwiGLU
• esm3::layers::blocks::UnifiedTransformerBlock
• esm3::layers::encode_inputs::EmbeddingBag
• esm3::layers::encode_inputs::EncodeInputs
• esm3::layers::output_heads::ESM3Output
• esm3::layers::output_heads::OutputHeads
• esm3::layers::output_heads::RegressionHead
• esm3::layers::relative_position::RelativePositionEmbedding
• esm3::layers::transformer_stack::TransformerStack
• esm3::models::esm3::ESM3
• esm3::models::esm3::ESM3Config
• esm3::models::vqvae::StructureTokenDecoder
• esm3::models::vqvae::StructureTokenEncoder
• esm3::models::vqvae::VqVaeConfig
• esm3::pretrained::ESM3Runner
• esm3::pretrained::StructureEncoderRunner
• esm3::utils::affine3d::Affine3D
• esmc::layers::attention::MultiHeadAttention
• esmc::layers::blocks::SwiGLU
• esmc::layers::blocks::UnifiedTransformerBlock
• esmc::layers::geom_attention::GeometricReasoningOriginalImpl
• esmc::layers::regression_head::RegressionHead
• esmc::layers::rotary::RotaryEmbedding
• esmc::layers::transformer_stack::TransformerStack
• esmc::models::esmc::ESMC
• esmc::models::esmc::ESMCConfig
• esmc::models::esmc::ESMCOutput
• esmc::models::esmc::LogitsConfig
• esmc::models::esmc::LogitsOutput
• esmc::pretrained::ESMCRunner
• esmc::tokenization::TokenizerCollection
• esmc::tokenization::sequence_tokenizer::EsmSequenceTokenizer
• 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::DecLayerJ
• ligandmpnn::model::EncLayer
• ligandmpnn::model::ProteinMPNN
• ligandmpnn::model::ScoreOutput
• ligandmpnn::pmpnn_runner::ProteinMPNNRunner
• ligandmpnn::proteinfeatures::ProteinFeatures
• loader::LoadOptions
• loader::WeightSource
• plm_runner::ModelMetadata
• plm_runner::SpecialTokenLayout
• plm_runner::TokenBatch
• registry::ModelCard
• t5::runner::T5Runner
• t5::translator::ProstT5Translator
• types::ContactMap
• types::PseudoProbability

Enums

• amplify::amplify_runner::AmplifyModels
• esm2::esm2_runner::ESM2Models
• esm3::pretrained::ESM3Models
• esmc::models::esmc::ESMTokenizer
• esmc::models::esmc::FfnType
• esmc::pretrained::ESMCModels
• featurize::utilities::AAAtom
• featurize::utilities::Residue
• ligandmpnn::configs::ModelTypes
• ligandmpnn::pmpnn_runner::ProteinMPNNModels
• loader::Format
• registry::Family
• registry::ParityStatus
• registry::TokenizerSpec
• registry::VocabAlphabet
• t5::runner::T5Models
• t5::tokenizer::Direction
• t5::translator::ProstT5Models
• utils::residue_constants::AAAtom

Traits

• esmc::tokenization::sequence_tokenizer::EsmTokenizerBase
• featurize::StructureFeatures
• plm_runner::PlmRunner

Functions

• amplify::amplify::apply_rotary_emb
• amplify::amplify::precompute_freqs_cis
• device
• esm2::saprot_tokenizer::interleave
• esm3::tokenization::sasa::tokenize_sasa
• esm3::tokenization::sequence::decode_sequence
• esm3::tokenization::sequence::tokenize_sequence
• esm3::tokenization::ss8::tokenize_ss8
• esm3::tokenization::structure::tokenize_structure
• esmc::tokenization::get_model_tokenizers
• esmc::utils::constants::models::model_is_locally_supported
• esmc::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::linear_last_dim
• featurize::utilities::linspace
• featurize::utilities::linspace_f32
• featurize::utilities::topk_last_dim
• ligandmpnn::model::multinomial_sample
• loader::optional_prefix
• loader::var_builder_from_path
• plm_runner::additive_padding_mask
• plm_runner::attention_mask_fill_value
• plm_runner::pad_token_batch
• plm_runner::stack_padded
• plm_runner::zero_padded_rows
• registry::by_family
• registry::loadable
• registry::lookup
• registry::support_matrix_markdown
• t5::tokenizer::encode
• t5::tokenizer::encode_for_translation
• t5::tokenizer::replace_rare_residues
• t5::tokenizer::residue_char
• t5::tokenizer::residue_count
• t5::tokenizer::residue_id
• t5::tokenizer::three_di_char
• t5::tokenizer::three_di_id
• t5::tokenizer::vocab_id
• utils::residue_constants::atom14_to_atom37_for_residue
• utils::residue_constants::atom37_index
• utils::residue_constants::atom_order
• utils::residue_constants::chi_angles_atoms

Constants

• esm2::saprot_tokenizer::CHARS_PER_RESIDUE
• esm2::saprot_tokenizer::UNKNOWN_STATE
• esm3::layers::relative_position::BINS
• esm3::layers::relative_position::NUM_EMBEDDINGS
• esm3::models::vqvae::KNN
• esm3::pretrained::STRUCTURE_ENCODER_ID
• esm3::utils::constants::INTERPRO_PAD_TOKEN
• esm3::utils::constants::RESIDUE_PAD_TOKEN
• esm3::utils::constants::SASA_DISCRETIZATION_BOUNDARIES
• esm3::utils::constants::SASA_MASK_TOKEN
• esm3::utils::constants::SASA_PAD_TOKEN
• esm3::utils::constants::SASA_UNK_TOKEN
• esm3::utils::constants::SEQUENCE_BOS_TOKEN
• esm3::utils::constants::SEQUENCE_CHAINBREAK_TOKEN
• esm3::utils::constants::SEQUENCE_EOS_TOKEN
• esm3::utils::constants::SEQUENCE_MASK_TOKEN
• esm3::utils::constants::SEQUENCE_PAD_TOKEN
• esm3::utils::constants::SS8_MASK_TOKEN
• esm3::utils::constants::SS8_PAD_TOKEN
• esm3::utils::constants::SS8_UNK_TOKEN
• esm3::utils::constants::SS8_VOCAB
• esm3::utils::constants::STRUCTURE_BOS_TOKEN
• esm3::utils::constants::STRUCTURE_CHAINBREAK_TOKEN
• esm3::utils::constants::STRUCTURE_EOS_TOKEN
• esm3::utils::constants::STRUCTURE_MASK_TOKEN
• esm3::utils::constants::STRUCTURE_PAD_TOKEN
• esm3::utils::constants::STRUCTURE_UNDEFINED_TOKEN
• esm3::utils::constants::VQVAE_CODEBOOK_SIZE
• esmc::utils::constants::SQRT_3
• esmc::utils::constants::esm3::SEQUENCE_VOCAB
• esmc::utils::constants::models::ESM3_FUNCTION_DECODER_V0
• esmc::utils::constants::models::ESM3_OPEN_SMALL
• esmc::utils::constants::models::ESM3_OPEN_SMALL_ALIAS_1
• esmc::utils::constants::models::ESM3_OPEN_SMALL_ALIAS_2
• esmc::utils::constants::models::ESM3_OPEN_SMALL_ALIAS_3
• esmc::utils::constants::models::ESM3_STRUCTURE_DECODER_V0
• esmc::utils::constants::models::ESM3_STRUCTURE_ENCODER_V0
• esmc::utils::constants::models::ESMC_300M
• esmc::utils::constants::models::ESMC_600M
• esmc::utils::constants::physics::BB_COORDINATES
• esmc::utils::constants::physics::CA_CB_BOND_LENGTH
• esmc::utils::constants::physics::CA_C_BOND_LENGTH
• esmc::utils::constants::physics::N_CA_BOND_LENGTH
• esmc::utils::constants::physics::PEPTIDE_N_C_BOND_LENGTH
• featurize::utilities::ALPHABET
• registry::REGISTRY
• t5::tokenizer::AA_TO_FOLD_ID
• t5::tokenizer::EOS_ID
• t5::tokenizer::FOLD_TO_AA_ID
• t5::tokenizer::PAD_ID
• t5::tokenizer::THREE_DI_OFFSET
• t5::tokenizer::UNK_ID
• t5::tokenizer::VOCAB_SIZE
• utils::residue_constants::ATOM37_NAMES
• utils::residue_constants::NUM_ATOM37
• utils::residue_constants::NUM_RESIDUES