├── .gitignore ├── README.md ├── batch_run_cath.py ├── debugger.py ├── openfold ├── __init__.py ├── config.py ├── data │ ├── __init__.py │ ├── data_modules.py │ ├── data_pipeline.py │ ├── data_transforms.py │ ├── errors.py │ ├── feature_pipeline.py │ ├── input_pipeline.py │ └── parsers.py ├── model │ ├── __init__.py │ ├── conv.py │ ├── dropout.py │ ├── embedders.py │ ├── evoformer.py │ ├── gvp │ │ ├── __init__.py │ │ ├── features.py │ │ ├── gvp_encoder.py │ │ ├── gvp_gnn_encoder.py │ │ ├── gvp_modules.py │ │ ├── gvp_utils.py │ │ └── util.py │ ├── heads.py │ ├── model.py │ ├── outer_product_mean.py │ ├── pair_transition.py │ ├── primitives.py │ ├── seq_update.py │ ├── structure_module.py │ ├── triangular_attention.py │ └── triangular_multiplicative_update.py ├── np │ ├── __init__.py │ ├── protein.py │ ├── relax │ │ ├── __init__.py │ │ ├── amber_minimize.py │ │ ├── cleanup.py │ │ ├── relax.py │ │ └── utils.py │ └── residue_constants.py └── utils │ ├── __init__.py │ ├── argparse.py │ ├── callbacks.py │ ├── checkpointing.py │ ├── data_utils.py │ ├── exponential_moving_average.py │ ├── feats.py │ ├── import_weights.py │ ├── logger.py │ ├── loss.py │ ├── lr_schedulers.py │ ├── rigid_utils.py │ ├── seed.py │ ├── superimposition.py │ ├── suppress_output.py │ ├── tensor_utils.py │ └── validation_metrics.py ├── run_cath.py ├── script.sh ├── scripts ├── dllogger │ ├── CONTRIBUTING.md │ ├── LICENSE │ ├── README.md │ ├── dllogger │ │ ├── __init__.py │ │ └── logger.py │ ├── examples │ │ ├── dllogger_example.py │ │ ├── dllogger_singleton_example.py │ │ ├── example_resnet_log.json │ │ └── example_stdout_log.txt │ └── setup.py ├── environment.yml ├── eval.sh ├── install_third_party_dependencies.sh ├── md5sum.txt └── train.sh ├── train_cath.py └── yaml_config └── deterministic.yml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shichence/ProtSeed/HEAD/.gitignore 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