├── .gitignore ├── README.md ├── esm3 ├── esm │ ├── layers │ │ ├── attention.py │ │ ├── blocks.py │ │ ├── codebook.py │ │ ├── geom_attention.py │ │ ├── regression_head.py │ │ ├── rotary.py │ │ ├── structure_proj.py │ │ └── transformer_stack.py │ ├── models │ │ ├── esm3.py │ │ ├── function_decoder.py │ │ └── vqvae.py │ ├── pretrained.py │ ├── sdk │ │ └── api.py │ ├── tokenization │ │ ├── __init__.py │ │ ├── function_tokenizer.py │ │ ├── structure_tokenizer.py │ │ └── tokenizer_base.py │ └── utils │ │ ├── constants │ │ ├── esm3.py │ │ ├── models.py │ │ └── physics.py │ │ ├── encoding.py │ │ ├── function │ │ ├── encode_decode.py │ │ ├── interpro.py │ │ ├── lsh.py │ │ └── tfidf.py │ │ ├── misc.py │ │ ├── pmap.py │ │ ├── residue_constants.py │ │ ├── structure │ │ ├── affine3d.py │ │ ├── aligner.py │ │ ├── lddt.py │ │ ├── normalize_coordinates.py │ │ ├── predicted_aligned_error.py │ │ ├── protein_chain copy.py │ │ ├── protein_chain.py │ │ └── protein_structure.py │ │ └── types.py └── test_tokenize.py ├── foldseek ├── create_vqvae_training_data.py ├── extract_pdb_features.py ├── foldseek_v1 │ ├── encoder.pt │ ├── states.txt │ └── sub_score.mat ├── struct2states.py ├── struct2states_jsonl.py └── util.py ├── foldtoken ├── LICENSE.txt ├── data_interface.py ├── environment.yml ├── extract_vq_ids.py ├── extract_vq_ids_jsonl.py ├── images │ ├── 8vy8E.png │ ├── 8ybxR.png │ ├── foldtoken_logo.png │ ├── foldtoken_logo_black.png │ ├── foldtoken_logo_blue.png │ ├── logo.png │ └── screenshot.png ├── model_interface.py ├── reconstruct.py └── src │ ├── __init_.py │ ├── chroma │ ├── .DS_Store │ ├── constants │ │ ├── __init__.py │ │ ├── geometry.py │ │ ├── named_models.py │ │ └── sequence.py │ ├── data │ │ ├── .DS_Store │ │ ├── __init__.py │ │ ├── protein.py │ │ ├── system.py │ │ └── xcs.py │ ├── layers │ │ ├── __init__.py │ │ ├── attention.py │ │ ├── basic.py │ │ ├── complexity.py │ │ ├── conv.py │ │ ├── graph.py │ │ ├── linalg.py │ │ ├── norm.py │ │ ├── sde.py │ │ └── structure │ │ │ ├── __init__.py │ │ │ ├── backbone.py │ │ │ ├── conditioners.py │ │ │ ├── diffusion.py │ │ │ ├── geometry.py │ │ │ ├── hbonds.py │ │ │ ├── mvn.py │ │ │ ├── optimal_transport.py │ │ │ ├── potts.py │ │ │ ├── protein_graph.py │ │ │ ├── protein_graph_allatom.py │ │ │ ├── rmsd.py │ │ │ ├── sidechain.py │ │ │ ├── symmetry.py │ │ │ └── transforms.py │ └── utility │ │ ├── __init__.py │ │ ├── fetchdb.py │ │ ├── ngl.py │ │ ├── polyseq.py │ │ └── starparser.py │ ├── datasets │ ├── cath_dataset_struct.py │ └── pdb_dataset_struct.py │ ├── interface │ ├── data_interface.py │ └── model_interface.py │ ├── models │ ├── FoldToken4.py │ └── PiFold_sae.py │ ├── modules │ ├── FoldToken4_module.py │ ├── __init__.py │ ├── graph_transform.py │ ├── pifold_module_sae.py │ └── vq_modules.py │ └── tools │ ├── MLM_utils.py │ ├── affine_utils.py │ ├── convertor.py │ ├── encoding.py │ ├── geo_utils.py │ ├── logger.py │ ├── nerf.py │ ├── tensor_utils.py │ └── utils.py └── foldtoken5 ├── data_interface.py ├── extract_vq_ids.py ├── extract_vq_ids_jsonl.py ├── model_interface.py ├── pdb2jsonl.py ├── reconstruct.py ├── run.sh └── src ├── __init_.py ├── chroma ├── .DS_Store ├── constants │ ├── __init__.py │ ├── geometry.py │ ├── named_models.py │ └── sequence.py ├── data │ ├── .DS_Store │ ├── __init__.py │ ├── protein.py │ ├── system.py │ └── xcs.py ├── layers │ ├── __init__.py │ ├── attention.py │ ├── basic.py │ ├── complexity.py │ ├── conv.py │ ├── graph.py │ ├── linalg.py │ ├── norm.py │ ├── sde.py │ └── structure │ │ ├── __init__.py │ │ ├── backbone.py │ │ ├── conditioners.py │ │ ├── diffusion.py │ │ ├── geometry.py │ │ ├── hbonds.py │ │ ├── mvn.py │ │ ├── optimal_transport.py │ │ ├── potts.py │ │ ├── protein_graph.py │ │ ├── protein_graph_allatom.py │ │ ├── rmsd.py │ │ ├── sidechain.py │ │ ├── symmetry.py │ │ └── transforms.py └── utility │ ├── __init__.py │ ├── fetchdb.py │ ├── ngl.py │ ├── polyseq.py │ └── starparser.py ├── datasets ├── cath_dataset_struct.py └── pdb_dataset_struct.py ├── interface ├── data_interface.py └── model_interface.py ├── models └── FoldToken5.py ├── modules ├── FoldToken4_module_consist.py ├── FoldToken5_module.py ├── __init__.py └── vq_modules5.py └── tools ├── MLM_utils.py ├── affine_utils.py ├── convertor.py ├── encoding.py ├── geo_utils.py ├── logger.py ├── nerf.py ├── tensor_utils.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/A4Bio/FoldToken_open/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/A4Bio/FoldToken_open/HEAD/README.md -------------------------------------------------------------------------------- /esm3/esm/layers/attention.py: -------------------------------------------------------------------------------- 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