├── .gitignore ├── ColabNuFold.ipynb ├── LICENSE ├── README.md ├── nufold.py ├── nufold ├── NuFoldLogo.png ├── __init__.py ├── common │ ├── __init__.py │ ├── base_constants.py │ ├── nucleicacid.py │ └── stereo_chemical_props_rna.txt ├── config.py ├── data │ ├── __init__.py │ ├── data_pipeline.py │ ├── data_transforms.py │ ├── feature_pipeline.py │ ├── input_pipeline.py │ ├── mmcif_parsing.py │ └── parsers.py └── model │ ├── __init__.py │ ├── nufold.py │ └── openfold │ ├── __init__.py │ ├── checkpointing.py │ ├── dropout.py │ ├── embedders.py │ ├── evoformer.py │ ├── feats.py │ ├── heads.py │ ├── msa.py │ ├── outer_product_mean.py │ ├── pair_transition.py │ ├── primitives.py │ ├── rigid_utils.py │ ├── structure_module.py │ ├── template.py │ ├── tensor_utils.py │ ├── torchscript.py │ ├── triangular_attention.py │ └── triangular_multiplicative_update.py ├── run_nufold.py ├── test_input └── 2DER_C │ ├── 2DER_C.a3m │ ├── 2DER_C.fasta │ └── 2DER_C.single.ipknot.ss └── test_output └── 2DER_C 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