├── .gitignore ├── .idea └── .gitignore ├── LICENSE ├── README.md ├── bin └── README.md ├── demo ├── __init__.py ├── backend │ ├── __init__.py │ ├── server_manager.py │ ├── server_monitor.py │ └── servers │ │ ├── embedding_generation │ │ └── server.py │ │ └── retrieval │ │ ├── init_index.py │ │ └── server.py ├── config.yaml ├── modules │ ├── __init__.py │ ├── blocks.py │ ├── cli.py │ ├── compute_score.py │ ├── init_model.py │ ├── search.py │ └── tmalign.py ├── run.py └── run_pipeline.py ├── environment.sh ├── example ├── 8ac8.cif └── custom_db.fasta ├── faiss_index └── README.md ├── figure ├── colab-badge.svg └── img.jpg ├── model ├── ProTrek │ ├── protein_encoder.py │ ├── protrek_trimodal_model.py │ ├── structure_encoder.py │ └── text_encoder.py ├── abstract_model.py └── model_interface.py ├── requirements.txt ├── scripts └── generate_database.py ├── utils ├── constants.py ├── downloader.py ├── faiss_index.py ├── file_reader.py ├── foldseek_util.py ├── lr_scheduler.py ├── mpr.py └── server_tool.py └── weights └── README.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/ProTrek/HEAD/.gitignore -------------------------------------------------------------------------------- /.idea/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/ProTrek/HEAD/.idea/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/ProTrek/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/ProTrek/HEAD/README.md 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faiss index here -------------------------------------------------------------------------------- /figure/colab-badge.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/ProTrek/HEAD/figure/colab-badge.svg -------------------------------------------------------------------------------- /figure/img.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/ProTrek/HEAD/figure/img.jpg -------------------------------------------------------------------------------- /model/ProTrek/protein_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/westlake-repl/ProTrek/HEAD/model/ProTrek/protein_encoder.py -------------------------------------------------------------------------------- /model/ProTrek/protrek_trimodal_model.py: 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