├── CODE_OF_CONDUCT.md ├── LICENSE ├── ProteinAligner_downstream ├── .gitignore ├── esm_example.py ├── generator_train.csv ├── readme.md ├── regressor.pt ├── regressor.py └── utils.py ├── README.md ├── pretrain ├── __init__.py ├── bpe │ └── bpe_simple_vocab_16e6.txt.gz ├── data.py ├── dataloaders │ ├── __init__.py │ ├── joint_alternate_dataloader.py │ └── joint_dataloader.py ├── datasets │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-311.pyc │ │ ├── fasta_pdb_encoder_dataset.cpython-311.pyc │ │ └── fasta_text_encoder_dataset.cpython-311.pyc │ ├── fasta_pdb_dataset.py │ ├── fasta_pdb_encoder_dataset.py │ ├── fasta_pdb_encoder_dataset_pdb_sample.py │ ├── fasta_text_dataset.py │ ├── fasta_text_encoder_dataset.py │ └── fasta_text_encoder_dataset_pdb_sample.py ├── esm │ ├── __init__.py │ ├── axial_attention.py │ ├── constants.py │ ├── data.py │ ├── esmfold │ │ └── v1 │ │ │ ├── __init__.py │ │ │ ├── categorical_mixture.py │ │ │ ├── esmfold.py │ │ │ ├── misc.py │ │ │ ├── pretrained.py │ │ │ ├── tri_self_attn_block.py │ │ │ └── trunk.py │ ├── inverse_folding │ │ ├── __init__.py │ │ ├── features.py │ │ ├── gvp_encoder.py │ │ ├── gvp_modules.py │ │ ├── gvp_transformer.py │ │ ├── gvp_transformer_encoder.py │ │ ├── gvp_utils.py │ │ ├── multichain_util.py │ │ ├── transformer_decoder.py │ │ ├── transformer_layer.py │ │ └── util.py │ ├── model │ │ ├── __init__.py │ │ ├── esm1.py │ │ ├── esm2.py │ │ └── msa_transformer.py │ ├── modules.py │ ├── multihead_attention.py │ ├── pretrained.py │ ├── rotary_embedding.py │ └── version.py ├── models │ ├── __init__.py │ ├── helpers.py │ ├── multimodal_preprocessors.py │ ├── proteinbind_encoder_model.py │ └── transformer.py ├── train_joint_encoder.py └── utils │ ├── __pycache__ │ └── misc.cpython-311.pyc │ └── misc.py └── requirements.txt /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Alexiland/ProteinAligner/HEAD/CODE_OF_CONDUCT.md 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