Toggle Light / Dark / Auto color theme Toggle table of contents sidebar Index _ | B | C | D | E | F | G | I | M | N | O | P | Q | R | S | T | U | W _ __init__() (bio_embeddings.embed.BeplerEmbedder method) (bio_embeddings.embed.CPCProtEmbedder method) (bio_embeddings.embed.EmbedderInterface method) (bio_embeddings.embed.ESM1vEmbedder method) (bio_embeddings.embed.FastTextEmbedder method) (bio_embeddings.embed.GloveEmbedder method) (bio_embeddings.embed.PLUSRNNEmbedder method) (bio_embeddings.embed.ProtTransAlbertBFDEmbedder method) (bio_embeddings.embed.ProtTransBertBFDEmbedder method) (bio_embeddings.embed.ProtTransXLNetUniRef100Embedder method) (bio_embeddings.embed.SeqVecEmbedder method) (bio_embeddings.embed.UniRepEmbedder method) (bio_embeddings.embed.Word2VecEmbedder method) (bio_embeddings.extract.BasicAnnotationExtractor method) (bio_embeddings.mutagenesis.ProtTransBertBFDMutagenesis method) (bio_embeddings.project.PBTucker method) (bio_embeddings.project.PBTuckerModel method) (bio_embeddings.utilities.FileManagerInterface method) (bio_embeddings.utilities.FileSystemFileManager method) (bio_embeddings.utilities.QueryEmbeddingsFile method) B BasicAnnotationExtractor (class in bio_embeddings.extract) BeplerEmbedder (class in bio_embeddings.embed) bio_embeddings.embed module bio_embeddings.extract module bio_embeddings.mutagenesis module bio_embeddings.project module bio_embeddings.utilities module bio_embeddings.visualize module C check_required() (in module bio_embeddings.utilities) convert_list_of_enum_to_string() (in module bio_embeddings.utilities) CPCProtEmbedder (class in bio_embeddings.embed) create_directory() (bio_embeddings.utilities.FileManagerInterface method) (bio_embeddings.utilities.FileSystemFileManager method) create_file() (bio_embeddings.utilities.FileManagerInterface method) (bio_embeddings.utilities.FileSystemFileManager method) create_prefix() (bio_embeddings.utilities.FileManagerInterface method) (bio_embeddings.utilities.FileSystemFileManager method) create_stage() (bio_embeddings.utilities.FileManagerInterface method) (bio_embeddings.utilities.FileSystemFileManager method) D device (bio_embeddings.mutagenesis.ProtTransBertBFDMutagenesis attribute) E embed() (bio_embeddings.embed.BeplerEmbedder method) (bio_embeddings.embed.CPCProtEmbedder method) (bio_embeddings.embed.EmbedderInterface method) (bio_embeddings.embed.FastTextEmbedder method) (bio_embeddings.embed.GloveEmbedder method) (bio_embeddings.embed.OneHotEncodingEmbedder method) (bio_embeddings.embed.PLUSRNNEmbedder method) (bio_embeddings.embed.ProtTransXLNetUniRef100Embedder method) (bio_embeddings.embed.SeqVecEmbedder method) (bio_embeddings.embed.UniRepEmbedder method) (bio_embeddings.embed.Word2VecEmbedder method) embed_batch() (bio_embeddings.embed.CPCProtEmbedder method) (bio_embeddings.embed.EmbedderInterface method) (bio_embeddings.embed.PLUSRNNEmbedder method) (bio_embeddings.embed.ProtTransXLNetUniRef100Embedder method) embed_many() (bio_embeddings.embed.EmbedderInterface method) EmbedderInterface (class in bio_embeddings.embed) embedding_dimension (bio_embeddings.embed.BeplerEmbedder attribute) (bio_embeddings.embed.CPCProtEmbedder attribute) (bio_embeddings.embed.EmbedderInterface attribute) (bio_embeddings.embed.FastTextEmbedder attribute) (bio_embeddings.embed.GloveEmbedder attribute) (bio_embeddings.embed.OneHotEncodingEmbedder attribute) (bio_embeddings.embed.PLUSRNNEmbedder attribute) (bio_embeddings.embed.ProtTransAlbertBFDEmbedder attribute) (bio_embeddings.embed.ProtTransBertBFDEmbedder attribute) (bio_embeddings.embed.ProtTransXLNetUniRef100Embedder attribute) (bio_embeddings.embed.SeqVecEmbedder attribute) (bio_embeddings.embed.UniRepEmbedder attribute) (bio_embeddings.embed.Word2VecEmbedder attribute) ensemble_id (bio_embeddings.embed.ESM1vEmbedder attribute) ESM1bEmbedder (class in bio_embeddings.embed) ESM1vEmbedder (class in bio_embeddings.embed) ESMEmbedder (class in bio_embeddings.embed) exists() (bio_embeddings.utilities.FileManagerInterface method) (bio_embeddings.utilities.FileSystemFileManager method) F FastTextEmbedder (class in bio_embeddings.embed) FileManagerInterface (class in bio_embeddings.utilities) FileSystemFileManager (class in bio_embeddings.utilities) forward() (bio_embeddings.project.PBTuckerModel method) G get_annotations() (bio_embeddings.extract.BasicAnnotationExtractor method) get_device() (in module bio_embeddings.utilities) get_file() (bio_embeddings.utilities.FileManagerInterface method) (bio_embeddings.utilities.FileSystemFileManager method) get_file_manager() (in module bio_embeddings.utilities) get_k_nearest_neighbours() (in module bio_embeddings.extract) get_model_directories_from_zip() (in module bio_embeddings.utilities) get_model_file() (in module bio_embeddings.utilities) get_secondary_structure() (bio_embeddings.extract.BasicAnnotationExtractor method) get_sequence_probabilities() (bio_embeddings.mutagenesis.ProtTransBertBFDMutagenesis method) get_subcellular_location() (bio_embeddings.extract.BasicAnnotationExtractor method) GloveEmbedder (class in bio_embeddings.embed) I InvalidParameterError M model (bio_embeddings.mutagenesis.ProtTransBertBFDMutagenesis attribute) module bio_embeddings.embed bio_embeddings.extract bio_embeddings.mutagenesis bio_embeddings.project bio_embeddings.utilities bio_embeddings.visualize N name (bio_embeddings.embed.BeplerEmbedder attribute) (bio_embeddings.embed.CPCProtEmbedder attribute) (bio_embeddings.embed.EmbedderInterface attribute) (bio_embeddings.embed.ESM1bEmbedder attribute) (bio_embeddings.embed.ESM1vEmbedder attribute) (bio_embeddings.embed.ESMEmbedder attribute) (bio_embeddings.embed.FastTextEmbedder attribute) (bio_embeddings.embed.GloveEmbedder attribute) (bio_embeddings.embed.OneHotEncodingEmbedder attribute) (bio_embeddings.embed.PLUSRNNEmbedder attribute) (bio_embeddings.embed.ProtTransAlbertBFDEmbedder attribute) (bio_embeddings.embed.ProtTransBertBFDEmbedder attribute) (bio_embeddings.embed.ProtTransT5BFDEmbedder attribute) (bio_embeddings.embed.ProtTransT5UniRef50Embedder attribute) (bio_embeddings.embed.ProtTransT5XLU50Embedder attribute) (bio_embeddings.embed.ProtTransXLNetUniRef100Embedder attribute) (bio_embeddings.embed.SeqVecEmbedder attribute) (bio_embeddings.embed.UniRepEmbedder attribute) (bio_embeddings.embed.Word2VecEmbedder attribute) (bio_embeddings.project.PBTucker attribute) necessary_directories (bio_embeddings.embed.EmbedderInterface attribute) (bio_embeddings.embed.ProtTransXLNetUniRef100Embedder attribute) necessary_files (bio_embeddings.embed.BeplerEmbedder attribute) (bio_embeddings.embed.CPCProtEmbedder attribute) (bio_embeddings.embed.EmbedderInterface attribute) (bio_embeddings.embed.FastTextEmbedder attribute) (bio_embeddings.embed.GloveEmbedder attribute) (bio_embeddings.embed.PLUSRNNEmbedder attribute) (bio_embeddings.embed.SeqVecEmbedder attribute) (bio_embeddings.embed.Word2VecEmbedder attribute) (bio_embeddings.extract.BasicAnnotationExtractor attribute) number_of_layers (bio_embeddings.embed.BeplerEmbedder attribute) (bio_embeddings.embed.CPCProtEmbedder attribute) (bio_embeddings.embed.EmbedderInterface attribute) (bio_embeddings.embed.FastTextEmbedder attribute) (bio_embeddings.embed.GloveEmbedder attribute) (bio_embeddings.embed.OneHotEncodingEmbedder attribute) (bio_embeddings.embed.PLUSRNNEmbedder attribute) (bio_embeddings.embed.ProtTransAlbertBFDEmbedder attribute) (bio_embeddings.embed.ProtTransBertBFDEmbedder attribute) (bio_embeddings.embed.ProtTransXLNetUniRef100Embedder attribute) (bio_embeddings.embed.SeqVecEmbedder attribute) (bio_embeddings.embed.UniRepEmbedder attribute) (bio_embeddings.embed.Word2VecEmbedder attribute) O OneHotEncodingEmbedder (class in bio_embeddings.embed) P pairwise_distance_matrix_from_embeddings_and_annotations() (in module bio_embeddings.extract) PBTucker (class in bio_embeddings.project) PBTuckerModel (class in bio_embeddings.project) plot_mutagenesis() (in module bio_embeddings.visualize) PLUSRNNEmbedder (class in bio_embeddings.embed) probabilities_as_dataframe() (in module bio_embeddings.mutagenesis) project_reduced_embedding() (bio_embeddings.project.PBTucker method) ProtTransAlbertBFDEmbedder (class in bio_embeddings.embed) ProtTransBertBFDEmbedder (class in bio_embeddings.embed) ProtTransBertBFDMutagenesis (class in bio_embeddings.mutagenesis) ProtTransT5BFDEmbedder (class in bio_embeddings.embed) ProtTransT5UniRef50Embedder (class in bio_embeddings.embed) ProtTransT5XLU50Embedder (class in bio_embeddings.embed) ProtTransXLNetUniRef100Embedder (class in bio_embeddings.embed) Q query_new_id() (bio_embeddings.utilities.QueryEmbeddingsFile method) query_original_id() (bio_embeddings.utilities.QueryEmbeddingsFile method) QueryEmbeddingsFile (class in bio_embeddings.utilities) R read_fasta() (in module bio_embeddings.utilities) read_mapping_file() (in module bio_embeddings.utilities) reduce_per_protein() (bio_embeddings.embed.BeplerEmbedder static method) (bio_embeddings.embed.CPCProtEmbedder static method) (bio_embeddings.embed.EmbedderInterface static method) (bio_embeddings.embed.FastTextEmbedder static method) (bio_embeddings.embed.GloveEmbedder static method) (bio_embeddings.embed.OneHotEncodingEmbedder static method) (bio_embeddings.embed.PLUSRNNEmbedder static method) (bio_embeddings.embed.ProtTransXLNetUniRef100Embedder static method) (bio_embeddings.embed.SeqVecEmbedder static method) (bio_embeddings.embed.UniRepEmbedder static method) (bio_embeddings.embed.Word2VecEmbedder static method) reindex_h5_file() (in module bio_embeddings.utilities) reindex_sequences() (in module bio_embeddings.utilities) render_3D_scatter_plotly() (in module bio_embeddings.visualize) render_scatter_plotly() (in module bio_embeddings.visualize) run() (in module bio_embeddings.mutagenesis) S save_plotly_figure_to_html() (in module bio_embeddings.visualize) SeqVecEmbedder (class in bio_embeddings.embed) T tokenizer (bio_embeddings.mutagenesis.ProtTransBertBFDMutagenesis attribute) training (bio_embeddings.project.PBTuckerModel attribute) tsne_reduce() (in module bio_embeddings.project) U umap_reduce() (in module bio_embeddings.project) UniRepEmbedder (class in bio_embeddings.embed) W Word2VecEmbedder (class in bio_embeddings.embed) write_fasta_file() (in module bio_embeddings.utilities)