├── .dockerignore ├── .gitignore ├── .gitlab-ci.yml ├── CHANGELOG.md ├── Dockerfile ├── LICENSE.md ├── README.md ├── bio_embeddings ├── __init__.py ├── align │ ├── __init__.py │ ├── deepblast.py │ ├── mmseqs2.py │ └── pipeline.py ├── bio_embeddings_schema.json ├── embed │ ├── __init__.py │ ├── bepler_embedder.py │ ├── cpcprot_embedder.py │ ├── embedder_interfaces.py │ ├── esm_embedder.py │ ├── fasttext_embedder.py │ ├── glove_embedder.py │ ├── one_hot_encoding_embedder.py │ ├── pipeline.py │ ├── plus_rnn_embedder.py │ ├── prottrans_albert_bfd_embedder.py │ ├── prottrans_base_embedder.py │ ├── prottrans_bert_bfd_embedder.py │ ├── prottrans_t5_embedder.py │ ├── prottrans_xlnet_uniref100_embedder.py │ ├── seqvec_embedder.py │ ├── unirep_embedder.py │ └── word2vec_embedder.py ├── extract │ ├── __init__.py │ ├── annotations │ │ ├── __init__.py │ │ ├── binding_residues.py │ │ ├── conservation.py │ │ ├── disorder.py │ │ ├── location.py │ │ ├── membrane.py │ │ ├── membrane_residues.py │ │ └── secondary_structure.py │ ├── basic │ │ ├── __init__.py │ │ ├── annotation_inference_models.py │ │ └── basic_annotation_extractor.py │ ├── bindEmbed21 │ │ ├── __init__.py │ │ ├── bindEmbed21DL_annotation_extractor.py │ │ ├── bindEmbed21HBI_annotation_extractor.py │ │ └── binding_residues_cnn.py │ ├── light_attention │ │ ├── __init__.py │ │ ├── light_attention_annotation_extractor.py │ │ └── light_attention_model.py │ ├── pipeline.py │ ├── prott5cons │ │ ├── __init__.py │ │ ├── conservation_cnn.py │ │ └── prot_t5_cons_annotation_extractor.py │ ├── tmbed │ │ ├── __init__.py │ │ ├── tmbed_annotation_extractor.py │ │ ├── tmbed_cnn.py │ │ └── tmbed_viterbi.py │ └── unsupervised_utilities.py ├── mutagenesis │ ├── __init__.py │ ├── constants.py │ ├── pipeline.py │ └── protbert_bfd.py ├── project │ ├── __init__.py │ ├── pb_tucker.py │ ├── pipeline.py │ ├── tsne.py │ └── umap.py ├── utilities │ ├── __init__.py │ ├── backports.py │ ├── bisect_embedder_ram.py │ ├── cli.py │ ├── config.py │ ├── defaults.yml │ ├── exceptions.py │ ├── filemanagers │ │ ├── FileManagerInterface.py │ │ ├── FileSystemFileManager.py │ │ └── __init__.py │ ├── helpers.py │ ├── model_size_impl.py │ ├── model_size_main.py │ ├── model_size_old.py │ ├── pipeline.py │ └── remote_file_retriever.py └── visualize │ ├── __init__.py │ ├── mutagenesis.py │ ├── pipeline.py │ └── plotly_plots.py ├── docs ├── CNAME ├── Makefile ├── api │ ├── bio_embeddings.embed.md │ ├── bio_embeddings.extract.md │ ├── bio_embeddings.mutagenesis.md │ ├── bio_embeddings.project.md │ ├── bio_embeddings.utilities.md │ ├── bio_embeddings.visualize.md │ └── index.md ├── conf.py ├── contributing │ ├── embedder.md │ ├── extract.md │ ├── index.md │ └── setup.md ├── index.md ├── make.bat ├── notebooks ├── notebooks.md └── parameter_blueprints.md ├── examples ├── README.md ├── advanced_use_case │ ├── config.yml │ └── fasta.fa ├── bindEmbed21 │ ├── config.yml │ └── sequences.fasta ├── cath │ ├── cath_classes_S35.csv │ └── config.yml ├── deepblast │ ├── cath-db.csv │ ├── cath-db.fasta │ ├── cath-db.h5 │ ├── config_knn.yml │ ├── config_pairings_file.yml │ ├── mini-cath.fasta │ └── pairings.csv ├── deeploc │ ├── config.yml │ ├── deeploc_annotations.csv │ └── deeploc_data.fasta ├── disprot │ ├── config.yml │ ├── disordercdhit.fasta │ └── disprot_2019_09_labelled_0.2_0.8.csv ├── docker │ ├── annotation_file.csv │ ├── config.yml │ └── fasta.fa ├── goPredSim │ ├── config.yml │ └── sequences.fasta ├── goPredSim_prottrans_bert_bfd │ ├── config.yml │ └── sequences.fasta ├── light_attention │ ├── config.yml │ └── fasta.fa ├── mmseqs_profile │ ├── config.yml │ ├── large.fasta │ ├── sequences.fasta │ └── tiny.fasta ├── mmseqs_simple │ ├── config.yml │ ├── deeploc_data.fasta │ └── sequences.fasta ├── mutagenesis │ ├── config.yml │ └── sequences.fasta ├── parameters_blueprint.yml ├── supervised_annotation_extraction │ ├── config.yml │ └── fasta.fa ├── tucker │ ├── cath_annotations_class.csv │ ├── make_annotation.py │ ├── tucker_cath.fasta │ └── tucker_cath.yml ├── unsupervised_annotation_extraction │ ├── config.yml │ ├── disprot_2019_09_labelled_0.2_0.8_filtered.csv │ ├── disprot_seqvec_reduced_embeddings_file.h5 │ └── fasta.fa ├── use_case_one │ ├── annotation_file.csv │ ├── config.yml │ └── fasta.fa ├── use_case_three │ ├── annotations_1.csv │ ├── annotations_2.csv │ ├── config.yml │ ├── dummy_fasta.fa │ ├── mapping_file.csv │ └── reduced_embeddings_file.h5 └── use_case_two │ ├── config.yml │ ├── fasta.fa │ └── md5_annotation_file.csv ├── notebooks ├── README.md ├── deeploc_machine_learning.ipynb ├── deeploc_visualizations.ipynb ├── embed_custom_sequence.ipynb ├── embed_fasta_sequences.ipynb ├── extract_localization_from_ProtBert_using_light_attention.ipynb ├── extract_supervised_from_seqvec.ipynb ├── goPredSim.ipynb ├── open_embedding_file.ipynb ├── pairwise_distances_and_nearest_neighbours.ipynb ├── per_amino_acid_embedding_visualization.ipynb ├── project_visualize_custom_embeddings.ipynb ├── project_visualize_pipeline_embeddings.ipynb ├── reindex_h5_file.ipynb └── remove_identifiers_from_annotation_file.ipynb ├── poetry.lock ├── pyproject.toml ├── tasks.py ├── test-data ├── bindEmbed21HBI │ └── Q9RN60_hit.tsv ├── bonsai │ ├── .gitignore │ ├── Readme.md │ ├── annotations.csv │ ├── gopredsim.yml │ ├── knn_reference.fasta │ ├── knn_reference.h5 │ ├── knn_reference_embed.yml │ ├── make_reference.py │ ├── run.sh │ └── sequences.fasta ├── embed_config_mixup.yml ├── embeddings.npz ├── esm1v_missing_ensemble_id.yml ├── illegal_amino_acids.fasta ├── mapping_file.csv ├── mutagenesis │ ├── plot_mutagenesis.py │ └── probabilities.csv ├── reference-embeddings │ ├── bepler.npz │ ├── cpcprot.npz │ ├── esm.npz │ ├── esm1b.npz │ ├── esm1v.npz │ ├── fasttext.npz │ ├── glove.npz │ ├── input.fasta │ ├── one_hot_encoding.npz │ ├── pb_tucker.npz │ ├── plus_rnn.npz │ ├── prottrans_albert_bfd.npz │ ├── prottrans_bert_bfd.npz │ ├── prottrans_t5_bfd.npz │ ├── prottrans_t5_uniref50.npz │ ├── prottrans_t5_xl_u50.npz │ ├── prottrans_xlnet_uniref100.npz │ ├── seqvec.npz │ ├── unirep.npz │ └── word2vec.npz ├── remapped_sequences_file.fasta ├── seqwence-protein.fasta ├── subcellular_location_new_hard_set.fasta ├── test_notebooks.py ├── titin_twice.fasta ├── transferred_annotations_file.csv ├── tucker_umap │ ├── .gitignore │ ├── compare.py │ ├── knn_reference.fasta │ ├── merged_annotation_file_bert.csv │ ├── merged_annotation_file_tucker.csv │ ├── plot_file_bert.html │ ├── plot_file_tucker.html │ ├── projected_tucker_config.yml │ └── reduced_embeddings_file.h5 └── unparsable.fasta ├── tests ├── __init__.py ├── shared │ └── __init__.py ├── test_annotation_extractor.py ├── test_bindEmbed21DL.py ├── test_bindEmbed21HBI.py ├── test_bio_embeddings_simple.py ├── test_conservation.py ├── test_deepblast.py ├── test_embed_pipeline.py ├── test_embedder_embedding.py ├── test_embedder_other.py ├── test_fasta_processing.py ├── test_hypothesis_bio.py ├── test_mmseqs2.py ├── test_mutagenesis.py ├── test_pipeline_global.py ├── test_seqvec_fallbacks.py ├── test_subcellular.py └── test_webserver.py ├── tox.ini └── webserver ├── Dockerfile.webserver ├── Dockerfile.worker ├── README.md ├── backend.py ├── celery_worker.py ├── database └── __init__.py ├── dev ├── cert.pem ├── key.pem └── nginx.conf ├── docker-compose.dev.yml ├── docker-compose.prod.yml ├── endpoints ├── __init__.py ├── annotations.py ├── embeddings.py ├── pipeline.py ├── request_models.py ├── status.py ├── structure.py ├── task_interface.py └── utils.py ├── requirements.txt ├── static ├── index.css ├── index.js ├── jquery.min.js ├── semantic.min.css └── semantic.min.js ├── tasks ├── __init__.py ├── colabfold.py ├── pipeline.py ├── prott5_annotations.py ├── prott5_embeddings.py ├── prott5_residue_landscape_annotations.py └── template_configs │ └── annotations_from_prott5.yml ├── templates └── index.html ├── test_backend.sh ├── test_celery.sh ├── utilities ├── configuration.py └── parsers.py └── 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