├── README.MD ├── all_data └── RAbD_H3 │ ├── test.json │ └── test_processed │ ├── _metainfo │ └── part_0.pkl ├── data ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-311.pyc │ ├── esm_utils.cpython-311.pyc │ └── pdb_utils.cpython-311.pyc ├── download.py ├── esm_utils.py ├── pdb_utils.py ├── split.py └── utils.py ├── dataset ├── __init__.py └── dataset.py ├── eval.py ├── evaluation ├── TMscore ├── TMscore.cpp ├── __init__.py ├── ddg │ ├── data │ │ └── model.pt │ ├── models │ │ ├── __pycache__ │ │ │ ├── attention.cpython-311.pyc │ │ │ ├── common.cpython-311.pyc │ │ │ ├── predictor.cpython-311.pyc │ │ │ └── residue.cpython-311.pyc │ │ ├── attention.py │ │ ├── common.py │ │ ├── predictor.py │ │ └── residue.py │ └── utils │ │ ├── __pycache__ │ │ ├── data.cpython-311.pyc │ │ ├── misc.cpython-311.pyc │ │ └── protein.cpython-311.pyc │ │ ├── data.py │ │ ├── misc.py │ │ └── protein.py ├── evaluator.py ├── pred_ddg.py ├── rmsd.py └── tm_score.py ├── models ├── __init__.py ├── featurizers.py ├── geometry.py ├── initializers.py ├── modules.py ├── nerf.py ├── refiners.py └── vonmises.py ├── requirements.txt ├── results └── cdrh3 │ └── H3_refine │ └── checkpoint │ └── best.ckpt ├── train_design.py ├── train_init.py ├── train_refine.py ├── trainers ├── __init__.py ├── gentrainer.py └── trainer.py └── utils ├── __init__.py └── utils.py /README.MD: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EDAPINENUT/GeoAB/HEAD/README.MD -------------------------------------------------------------------------------- /all_data/RAbD_H3/test.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EDAPINENUT/GeoAB/HEAD/all_data/RAbD_H3/test.json -------------------------------------------------------------------------------- /all_data/RAbD_H3/test_processed/_metainfo: -------------------------------------------------------------------------------- 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