| """Ordered, residue-aware protein embedding utilities.""" |
|
|
| from .feature_runs import embed_into_features |
| from .pooling import ( |
| POOLING_NAMES, POOLING_SEMANTICS_TOKENS, TOKEN_POOLING_NAMES, Pooler, pagerank_weights, pool_token_rows, |
| ) |
| from .runner import ( |
| EmbeddingMixin, |
| embed_dataset, |
| iter_fasta, |
| parse_fasta, |
| select_hidden_state_embeddings, |
| ) |
| from .storage import ( |
| DEFAULT_SHARD_SIZE, |
| append_sqlite_records, |
| convert_legacy_sqlite, |
| garbage_collect_safetensors_generations, |
| initialize_sqlite_run, |
| load_legacy_pth, |
| load_result, |
| load_safetensors_result, |
| load_sqlite_result, |
| save_result, |
| save_safetensors_result, |
| save_sqlite_result, |
| tensor_sha256, |
| update_sqlite_run_metadata, |
| ) |
| from .taps import ( |
| HiddenTap, LayerAccumulator, ReducedTap, RowSelection, SparseResidueTap, StreamingTap, TapBatch, |
| ) |
| from .token_batches import BatchGeometry, TokenTapExecutor, plan_geometry_batches, plan_token_batches |
| from .token_runs import embed_token_features |
| from .tokens import ResidueVocabulary |
| from .types import ( |
| EmbeddingBatch, |
| EmbeddingInput, |
| EmbeddingRecord, |
| EmbeddingResult, |
| LazyTensorReference, |
| TapRecord, |
| TapResult, |
| TapRunReceipt, |
| TensorValue, |
| ) |
|
|
|
|
| __all__ = [ |
| "DEFAULT_SHARD_SIZE", |
| "POOLING_NAMES", |
| "POOLING_SEMANTICS_TOKENS", |
| "TOKEN_POOLING_NAMES", |
| "BatchGeometry", |
| "EmbeddingBatch", |
| "EmbeddingInput", |
| "EmbeddingMixin", |
| "EmbeddingRecord", |
| "EmbeddingResult", |
| "HiddenTap", |
| "LayerAccumulator", |
| "LazyTensorReference", |
| "Pooler", |
| "ReducedTap", |
| "ResidueVocabulary", |
| "RowSelection", |
| "SparseResidueTap", |
| "StreamingTap", |
| "TapBatch", |
| "TapRecord", |
| "TapResult", |
| "TapRunReceipt", |
| "TensorValue", |
| "TokenTapExecutor", |
| "append_sqlite_records", |
| "convert_legacy_sqlite", |
| "embed_dataset", |
| "embed_into_features", |
| "embed_token_features", |
| "garbage_collect_safetensors_generations", |
| "initialize_sqlite_run", |
| "iter_fasta", |
| "load_legacy_pth", |
| "load_result", |
| "load_safetensors_result", |
| "load_sqlite_result", |
| "pagerank_weights", |
| "parse_fasta", |
| "plan_geometry_batches", |
| "plan_token_batches", |
| "pool_token_rows", |
| "save_result", |
| "save_safetensors_result", |
| "save_sqlite_result", |
| "select_hidden_state_embeddings", |
| "tensor_sha256", |
| "update_sqlite_run_metadata", |
| ] |
|
|
