├── README.md ├── carbonmatrix ├── __init__.py ├── common │ ├── __init__.py │ ├── default_rigids.json │ ├── operator.py │ ├── residue_constants.py │ └── utils.py ├── data │ ├── __init__.py │ ├── base_dataset.py │ ├── dataset.py │ ├── esm.py │ ├── mmcif_parsing.py │ ├── parser.py │ ├── pdbio.py │ ├── seq.py │ ├── transform_factory.py │ ├── transforms.py │ └── transforms_lm.py ├── model │ ├── __init__.py │ ├── atom.py │ ├── baseformer.py │ ├── carbonnovo.py │ ├── common_modules.py │ ├── folding.py │ ├── head.py │ ├── head_factory.py │ ├── inverseformer.py │ ├── lm │ │ ├── __pycache__ │ │ │ ├── model_lm.cpython-311.pyc │ │ │ ├── multihead_attention.cpython-311.pyc │ │ │ ├── pretrained.cpython-311.pyc │ │ │ ├── rotary_embedding.cpython-311.pyc │ │ │ └── transformer.cpython-311.pyc │ │ ├── model_lm.py │ │ ├── multihead_attention.py │ │ ├── pretrained.py │ │ ├── rotary_embedding.py │ │ └── transformer.py │ ├── mpnn.py │ ├── quat_affine.py │ ├── r3.py │ ├── seqformer.py │ ├── sidechain.py │ └── utils.py └── sde │ ├── __init__.py │ ├── igso3.py │ ├── r3_diffuser.py │ ├── se3_diffuser.py │ ├── so3_diffuser.py │ ├── transforms.py │ └── utils.py ├── config ├── inference_carbonnovo.yaml ├── model │ └── carbonnovo.yaml └── transforms │ └── carbonnovo_inference.yaml ├── predict.py └── requirements.txt /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CarbonMatrixLab/carbonnovo/HEAD/README.md -------------------------------------------------------------------------------- /carbonmatrix/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /carbonmatrix/common/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /carbonmatrix/common/default_rigids.json: 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