├── README.md ├── RF2Lite-cu121-linux.yml ├── RF2Lite-linux.yml ├── SE3Transformer ├── .dockerignore ├── .gitignore ├── 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 │ │ ├── .basis.py.un~ │ │ ├── .transformer.py.un~ │ │ ├── __init__.py │ │ ├── basis.py │ │ ├── fiber.py │ │ ├── layers │ │ │ ├── .attention.py.un~ │ │ │ ├── .convolution.py.un~ │ │ │ ├── __init__.py │ │ │ ├── attention.py │ │ │ ├── convolution.py │ │ │ ├── convolution.py~ │ │ │ ├── linear.py │ │ │ ├── norm.py │ │ │ └── pooling.py │ │ ├── transformer.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 ├── .README.un~ ├── 1318230at2759_735423at2759_i90.a3m ├── 1408540at2759_312952at2759_i95.a3m ├── 171695at2759_197562at2759_i95.a3m ├── P77499_P77689.fas ├── README ├── make_input_list.py └── negative.inputs └── networks ├── Attention_module.py ├── AuxiliaryPredictor.py ├── Embeddings.py ├── RoseTTAFoldModel.py ├── SE3_network.py ├── Track_module.py ├── arguments.py ├── constant.py ├── coords6d.py ├── data_loader.py ├── kinematics.py ├── loss.py ├── parsers.py ├── performance_benchmark.py ├── predict_complex.py ├── predict_complex_list.py ├── predict_complex_list_full.py ├── resnet.py ├── scheduler.py ├── trFold.py ├── train_multi_EMA.py ├── train_reference.py ├── util.py └── util_module.py /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/README.md -------------------------------------------------------------------------------- /RF2Lite-cu121-linux.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/RF2Lite-cu121-linux.yml -------------------------------------------------------------------------------- /RF2Lite-linux.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/RF2Lite-linux.yml -------------------------------------------------------------------------------- /SE3Transformer/.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/.dockerignore -------------------------------------------------------------------------------- /SE3Transformer/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/.gitignore -------------------------------------------------------------------------------- /SE3Transformer/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/Dockerfile -------------------------------------------------------------------------------- /SE3Transformer/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/LICENSE -------------------------------------------------------------------------------- /SE3Transformer/NOTICE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/NOTICE -------------------------------------------------------------------------------- /SE3Transformer/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/README.md -------------------------------------------------------------------------------- /SE3Transformer/images/se3-transformer.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/images/se3-transformer.png -------------------------------------------------------------------------------- /SE3Transformer/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/requirements.txt -------------------------------------------------------------------------------- /SE3Transformer/scripts/benchmark_inference.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/scripts/benchmark_inference.sh -------------------------------------------------------------------------------- /SE3Transformer/scripts/benchmark_train.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/scripts/benchmark_train.sh -------------------------------------------------------------------------------- /SE3Transformer/scripts/benchmark_train_multi_gpu.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/scripts/benchmark_train_multi_gpu.sh -------------------------------------------------------------------------------- /SE3Transformer/scripts/predict.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/scripts/predict.sh -------------------------------------------------------------------------------- /SE3Transformer/scripts/train.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/scripts/train.sh -------------------------------------------------------------------------------- /SE3Transformer/scripts/train_multi_gpu.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/scripts/train_multi_gpu.sh -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/data_loading/__init__.py: -------------------------------------------------------------------------------- 1 | from .qm9 import QM9DataModule 2 | -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/data_loading/data_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/data_loading/data_module.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/data_loading/qm9.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/data_loading/qm9.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/.basis.py.un~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/.basis.py.un~ -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/.transformer.py.un~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/.transformer.py.un~ -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/__init__.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/basis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/basis.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/fiber.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/fiber.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/.attention.py.un~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/.attention.py.un~ -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/.convolution.py.un~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/.convolution.py.un~ -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/__init__.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/attention.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/convolution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/convolution.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/convolution.py~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/convolution.py~ -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/linear.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/linear.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/norm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/norm.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/layers/pooling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/layers/pooling.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/transformer.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/model/transformer.py~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/model/transformer.py~ -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/arguments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/runtime/arguments.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/callbacks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/runtime/callbacks.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/gpu_affinity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/runtime/gpu_affinity.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/runtime/inference.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/loggers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/runtime/loggers.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/runtime/metrics.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/training.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/runtime/training.py -------------------------------------------------------------------------------- /SE3Transformer/se3_transformer/runtime/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/se3_transformer/runtime/utils.py -------------------------------------------------------------------------------- /SE3Transformer/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/setup.py -------------------------------------------------------------------------------- /SE3Transformer/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /SE3Transformer/tests/test_equivariance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/tests/test_equivariance.py -------------------------------------------------------------------------------- /SE3Transformer/tests/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/SE3Transformer/tests/utils.py -------------------------------------------------------------------------------- /example/.README.un~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/example/.README.un~ -------------------------------------------------------------------------------- /example/1318230at2759_735423at2759_i90.a3m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/example/1318230at2759_735423at2759_i90.a3m -------------------------------------------------------------------------------- /example/1408540at2759_312952at2759_i95.a3m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/example/1408540at2759_312952at2759_i95.a3m -------------------------------------------------------------------------------- /example/171695at2759_197562at2759_i95.a3m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/example/171695at2759_197562at2759_i95.a3m -------------------------------------------------------------------------------- /example/P77499_P77689.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/example/P77499_P77689.fas -------------------------------------------------------------------------------- /example/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/example/README -------------------------------------------------------------------------------- /example/make_input_list.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/example/make_input_list.py -------------------------------------------------------------------------------- /example/negative.inputs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/example/negative.inputs -------------------------------------------------------------------------------- /networks/Attention_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/Attention_module.py -------------------------------------------------------------------------------- /networks/AuxiliaryPredictor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/AuxiliaryPredictor.py -------------------------------------------------------------------------------- /networks/Embeddings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/Embeddings.py -------------------------------------------------------------------------------- /networks/RoseTTAFoldModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/RoseTTAFoldModel.py -------------------------------------------------------------------------------- /networks/SE3_network.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/SE3_network.py -------------------------------------------------------------------------------- /networks/Track_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/Track_module.py -------------------------------------------------------------------------------- /networks/arguments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/arguments.py -------------------------------------------------------------------------------- /networks/constant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/constant.py -------------------------------------------------------------------------------- /networks/coords6d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/coords6d.py -------------------------------------------------------------------------------- /networks/data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/data_loader.py -------------------------------------------------------------------------------- /networks/kinematics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/kinematics.py -------------------------------------------------------------------------------- /networks/loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/loss.py -------------------------------------------------------------------------------- /networks/parsers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/parsers.py -------------------------------------------------------------------------------- /networks/performance_benchmark.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/performance_benchmark.py -------------------------------------------------------------------------------- /networks/predict_complex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/predict_complex.py -------------------------------------------------------------------------------- /networks/predict_complex_list.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/predict_complex_list.py -------------------------------------------------------------------------------- /networks/predict_complex_list_full.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/predict_complex_list_full.py -------------------------------------------------------------------------------- /networks/resnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/resnet.py -------------------------------------------------------------------------------- /networks/scheduler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/scheduler.py -------------------------------------------------------------------------------- /networks/trFold.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/trFold.py -------------------------------------------------------------------------------- /networks/train_multi_EMA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/train_multi_EMA.py -------------------------------------------------------------------------------- /networks/train_reference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/train_reference.py -------------------------------------------------------------------------------- /networks/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/util.py -------------------------------------------------------------------------------- /networks/util_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SNU-CSSB/RF2-Lite/HEAD/networks/util_module.py --------------------------------------------------------------------------------