├── LICENSE ├── README.md ├── RF2na-linux.yml ├── SE3Transformer ├── Dockerfile ├── LICENSE ├── NOTICE ├── README.md ├── images │ └── se3-transformer.png ├── requirements.txt ├── scripts │ ├── benchmark_inference.sh │ ├── benchmark_train.sh │ ├── benchmark_train_multi_gpu.sh │ ├── predict.sh │ ├── train.sh │ └── train_multi_gpu.sh ├── se3_transformer │ ├── __init__.py │ ├── data_loading │ │ ├── __init__.py │ │ ├── data_module.py │ │ └── qm9.py │ ├── model │ │ ├── __init__.py │ │ ├── basis.py │ │ ├── fiber.py │ │ ├── layers │ │ │ ├── __init__.py │ │ │ ├── attention.py │ │ │ ├── convolution.py │ │ │ ├── linear.py │ │ │ ├── norm.py │ │ │ └── pooling.py │ │ └── transformer.py │ └── runtime │ │ ├── __init__.py │ │ ├── arguments.py │ │ ├── callbacks.py │ │ ├── gpu_affinity.py │ │ ├── inference.py │ │ ├── loggers.py │ │ ├── metrics.py │ │ ├── training.py │ │ └── utils.py ├── setup.py └── tests │ ├── __init__.py │ ├── test_equivariance.py │ └── utils.py ├── example ├── RNA.fa ├── dna_binding_protein.fa └── rna_binding_protein.fa ├── input_prep ├── make_protein_msa.sh ├── make_rna_msa.sh ├── merge_msa_prot_rna.py └── reprocess_rnac.pl ├── network ├── Attention_module.py ├── AuxiliaryPredictor.py ├── Embeddings.py ├── RoseTTAFoldModel.py ├── SE3_network.py ├── Track_module.py ├── arguments.py ├── chemical.py ├── coords6d.py ├── data_loader.py ├── ffindex.py ├── kinematics.py ├── loss.py ├── models.json ├── parsers.py ├── predict.py ├── resnet.py ├── scheduler.py ├── scoring.py ├── util.py └── util_module.py └── run_RF2NA.sh /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uw-ipd/RoseTTAFold2NA/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uw-ipd/RoseTTAFold2NA/HEAD/README.md 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