├── .gitignore ├── Joint_to_repacker.py ├── README.md ├── data ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-311.pyc │ ├── __init__.cpython-39.pyc │ ├── data.cpython-39.pyc │ ├── data_module.cpython-311.pyc │ ├── data_module.cpython-39.pyc │ ├── data_transform.cpython-311.pyc │ └── data_transform.cpython-39.pyc ├── add_dataset.py ├── builder_for_AL.py ├── data.py ├── data_module.py ├── data_transform.py ├── downlaod_chains.py ├── read_class.py ├── read_index.py ├── split_dataset.py └── test_cathtestset.py ├── demo ├── 5bvl.pdb └── processed_pdb.pkl ├── design └── CASP15_nocut.pkl ├── environment.yml ├── image └── dataspilt.png ├── model ├── AAindex1 ├── AngelResnet.py ├── Relax │ ├── RelaxEpacker.py │ └── __pycache__ │ │ └── RelaxEpacker.cpython-310.pyc ├── Rigid.py ├── __init__.py ├── __pycache__ │ ├── AngelResnet.cpython-310.pyc │ ├── AngelResnet.cpython-311.pyc │ ├── AngelResnet.cpython-37.pyc │ ├── AngelResnet.cpython-39.pyc │ ├── Joint_model_old.cpython-310.pyc │ ├── Rigid.cpython-310.pyc │ ├── Rigid.cpython-311.pyc │ ├── Rigid.cpython-37.pyc │ ├── Rigid.cpython-39.pyc │ ├── __init__.cpython-311.pyc │ ├── __init__.cpython-37.pyc │ ├── __init__.cpython-39.pyc │ ├── chems.cpython-310.pyc │ ├── chems.cpython-311.pyc │ ├── chems.cpython-37.pyc │ ├── chems.cpython-39.pyc │ ├── mesh_utils.cpython-310.pyc │ ├── mesh_utils.cpython-311.pyc │ ├── mesh_utils.cpython-37.pyc │ ├── mesh_utils.cpython-39.pyc │ ├── primitives.cpython-310.pyc │ ├── primitives.cpython-311.pyc │ ├── primitives.cpython-37.pyc │ ├── primitives.cpython-39.pyc │ ├── utils.cpython-310.pyc │ ├── utils.cpython-311.pyc │ ├── utils.cpython-37.pyc │ └── utils.cpython-39.pyc ├── chems.py ├── data │ ├── __pycache__ │ │ ├── data_pipeline.cpython-310.pyc │ │ ├── data_pipeline.cpython-37.pyc │ │ └── data_pipeline.cpython-39.pyc │ └── data_pipeline.py ├── mesh_utils.py ├── metrics.py ├── network │ ├── Embedding │ │ ├── Embeddings.py │ │ ├── __pycache__ │ │ │ ├── Embeddings.cpython-311.pyc │ │ │ ├── Embeddings.cpython-37.pyc │ │ │ ├── Embeddings.cpython-39.pyc │ │ │ ├── outer_product_mean.cpython-311.pyc │ │ │ ├── outer_product_mean.cpython-37.pyc │ │ │ ├── outer_product_mean.cpython-39.pyc │ │ │ ├── pair_trans.cpython-311.pyc │ │ │ ├── pair_trans.cpython-37.pyc │ │ │ └── pair_trans.cpython-39.pyc │ │ ├── outer_product_mean.py │ │ └── pair_trans.py │ ├── Generator.py │ ├── Joint_model.py │ ├── Repacker.py │ ├── Transformer.py │ ├── __pycache__ │ │ ├── Generator.cpython-310.pyc │ │ ├── Generator.cpython-311.pyc │ │ ├── Generator.cpython-37.pyc │ │ ├── Generator.cpython-39.pyc │ │ ├── Joint_model.cpython-310.pyc │ │ ├── Joint_model.cpython-311.pyc │ │ ├── Joint_model.cpython-39.pyc │ │ ├── Repacker.cpython-310.pyc │ │ ├── Repacker.cpython-311.pyc │ │ ├── Repacker.cpython-37.pyc │ │ ├── Repacker.cpython-39.pyc │ │ ├── Repacker_old.cpython-310.pyc │ │ ├── Transformer.cpython-310.pyc │ │ ├── Transformer.cpython-311.pyc │ │ ├── Transformer.cpython-37.pyc │ │ ├── Transformer.cpython-39.pyc │ │ ├── feats.cpython-310.pyc │ │ ├── feats.cpython-311.pyc │ │ ├── feats.cpython-37.pyc │ │ ├── feats.cpython-39.pyc │ │ ├── loss.cpython-310.pyc │ │ ├── loss.cpython-311.pyc │ │ ├── loss.cpython-37.pyc │ │ ├── loss.cpython-39.pyc │ │ ├── loss_old.cpython-310.pyc │ │ ├── minigpt.cpython-39.pyc │ │ ├── performer_pytorch.cpython-310.pyc │ │ ├── performer_pytorch.cpython-311.pyc │ │ ├── performer_pytorch.cpython-37.pyc │ │ ├── performer_pytorch.cpython-39.pyc │ │ ├── relax_protein.cpython-310.pyc │ │ ├── relax_protein.cpython-311.pyc │ │ ├── relax_protein.cpython-37.pyc │ │ ├── relax_protein.cpython-39.pyc │ │ ├── repackerloss.cpython-310.pyc │ │ ├── repackerloss.cpython-311.pyc │ │ ├── repackerloss.cpython-37.pyc │ │ ├── repackerloss.cpython-39.pyc │ │ ├── resnet.cpython-311.pyc │ │ ├── resnet.cpython-37.pyc │ │ ├── resnet.cpython-39.pyc │ │ └── util.cpython-310.pyc │ ├── feats.py │ ├── invariant_point_attention │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── __init__.cpython-37.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── invariant_point_attention.cpython-310.pyc │ │ │ ├── invariant_point_attention.cpython-311.pyc │ │ │ ├── invariant_point_attention.cpython-37.pyc │ │ │ └── invariant_point_attention.cpython-39.pyc │ │ ├── invariant_point_attention.py │ │ └── utils.py │ ├── loss.py │ ├── performer_pytorch.py │ ├── relax_protein.py │ ├── repackerloss.py │ ├── resnet.py │ ├── util.py │ └── utils │ │ ├── AAindex1 │ │ ├── utils_data.py │ │ ├── utils_logging.py │ │ └── utils_profiling.py ├── np │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-37.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── protein.cpython-310.pyc │ │ ├── protein.cpython-311.pyc │ │ ├── protein.cpython-37.pyc │ │ ├── protein.cpython-39.pyc │ │ ├── residue_constants.cpython-310.pyc │ │ ├── residue_constants.cpython-311.pyc │ │ ├── residue_constants.cpython-37.pyc │ │ └── residue_constants.cpython-39.pyc │ ├── protein.py │ ├── relax │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── __init__.cpython-37.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── amber_minimize.cpython-310.pyc │ │ │ ├── amber_minimize.cpython-311.pyc │ │ │ ├── amber_minimize.cpython-37.pyc │ │ │ ├── amber_minimize.cpython-39.pyc │ │ │ ├── cleanup.cpython-310.pyc │ │ │ ├── cleanup.cpython-311.pyc │ │ │ ├── cleanup.cpython-37.pyc │ │ │ ├── cleanup.cpython-39.pyc │ │ │ ├── relax.cpython-310.pyc │ │ │ ├── relax.cpython-311.pyc │ │ │ ├── relax.cpython-37.pyc │ │ │ ├── relax.cpython-39.pyc │ │ │ ├── utils.cpython-310.pyc │ │ │ ├── utils.cpython-37.pyc │ │ │ └── utils.cpython-39.pyc │ │ ├── amber_minimize.py │ │ ├── cleanup.py │ │ ├── relax.py │ │ └── utils.py │ ├── residue_constants.py │ └── stereo_chemical_props.txt ├── primitives.py └── utils.py ├── requirements.txt ├── 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