├── .gitignore ├── LICENSE ├── README.md ├── best_model ├── __init__.py ├── fold1 │ ├── __init__.py │ └── checkpoint.pth.tar ├── fold2 │ ├── __init__.py │ └── checkpoint.pth.tar ├── fold3 │ ├── __init__.py │ └── checkpoint.pth.tar ├── fold4 │ ├── __init__.py │ └── checkpoint.pth.tar └── fold5 │ └── checkpoint.pth.tar ├── data_processing ├── Extract_Interface.py ├── Feature_Processing.py ├── Prepare_Input.py ├── Single_Dataset.py ├── __init__.py └── collate_fn.py ├── example ├── __init__.py ├── input │ ├── correct.pdb │ └── incorrect.pdb └── output │ ├── multi │ ├── Predict.txt │ ├── Predict_sort.txt │ ├── correct │ │ ├── Input.linterface │ │ ├── Input.npz │ │ ├── Input.pdb │ │ └── Input.rinterface │ └── incorrect │ │ ├── Input.linterface │ │ ├── Input.npz │ │ ├── Input.pdb │ │ └── Input.rinterface │ ├── single │ ├── Input.linterface │ ├── Input.npz │ ├── Input.pdb │ ├── Input.rinterface │ └── Predict.txt │ └── visualize │ ├── Input.linterface │ ├── Input.npz │ ├── Input.pdb │ ├── Input.rinterface │ ├── attention1.npy │ ├── attention1_ligand.pdb │ ├── attention1_receptor.pdb │ ├── attention2.npy │ ├── attention2_ligand.pdb │ └── attention2_receptor.pdb ├── figure ├── attention.jpeg ├── network.png └── protocal.jpeg ├── main.py ├── model ├── GNN_Model.py ├── __init__.py └── layers.py ├── ops ├── Timer_Control.py ├── __init__.py ├── argparser.py ├── os_operation.py └── train_utils.py ├── predict ├── __init__.py ├── predict_multi_input.py ├── predict_single_input.py └── visualize_attention.py └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- 1 | .idea/ 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/README.md -------------------------------------------------------------------------------- /best_model/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /best_model/fold1/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /best_model/fold1/checkpoint.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/best_model/fold1/checkpoint.pth.tar -------------------------------------------------------------------------------- /best_model/fold2/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /best_model/fold2/checkpoint.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/best_model/fold2/checkpoint.pth.tar -------------------------------------------------------------------------------- /best_model/fold3/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /best_model/fold3/checkpoint.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/best_model/fold3/checkpoint.pth.tar -------------------------------------------------------------------------------- /best_model/fold4/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /best_model/fold4/checkpoint.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/best_model/fold4/checkpoint.pth.tar -------------------------------------------------------------------------------- /best_model/fold5/checkpoint.pth.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/best_model/fold5/checkpoint.pth.tar -------------------------------------------------------------------------------- /data_processing/Extract_Interface.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/data_processing/Extract_Interface.py -------------------------------------------------------------------------------- /data_processing/Feature_Processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/data_processing/Feature_Processing.py -------------------------------------------------------------------------------- /data_processing/Prepare_Input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/data_processing/Prepare_Input.py -------------------------------------------------------------------------------- /data_processing/Single_Dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/data_processing/Single_Dataset.py -------------------------------------------------------------------------------- /data_processing/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/data_processing/__init__.py -------------------------------------------------------------------------------- /data_processing/collate_fn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/data_processing/collate_fn.py -------------------------------------------------------------------------------- /example/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /example/input/correct.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/input/correct.pdb -------------------------------------------------------------------------------- /example/input/incorrect.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/input/incorrect.pdb -------------------------------------------------------------------------------- /example/output/multi/Predict.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/Predict.txt -------------------------------------------------------------------------------- /example/output/multi/Predict_sort.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/Predict_sort.txt -------------------------------------------------------------------------------- /example/output/multi/correct/Input.linterface: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/correct/Input.linterface -------------------------------------------------------------------------------- /example/output/multi/correct/Input.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/correct/Input.npz -------------------------------------------------------------------------------- /example/output/multi/correct/Input.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/correct/Input.pdb -------------------------------------------------------------------------------- /example/output/multi/correct/Input.rinterface: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/correct/Input.rinterface -------------------------------------------------------------------------------- /example/output/multi/incorrect/Input.linterface: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/incorrect/Input.linterface -------------------------------------------------------------------------------- /example/output/multi/incorrect/Input.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/incorrect/Input.npz -------------------------------------------------------------------------------- /example/output/multi/incorrect/Input.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/incorrect/Input.pdb -------------------------------------------------------------------------------- /example/output/multi/incorrect/Input.rinterface: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/multi/incorrect/Input.rinterface -------------------------------------------------------------------------------- /example/output/single/Input.linterface: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/single/Input.linterface -------------------------------------------------------------------------------- /example/output/single/Input.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/single/Input.npz -------------------------------------------------------------------------------- /example/output/single/Input.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/single/Input.pdb -------------------------------------------------------------------------------- /example/output/single/Input.rinterface: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/single/Input.rinterface -------------------------------------------------------------------------------- /example/output/single/Predict.txt: -------------------------------------------------------------------------------- 1 | Input Score 2 | correct.pdb 0.9969 3 | -------------------------------------------------------------------------------- /example/output/visualize/Input.linterface: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/Input.linterface -------------------------------------------------------------------------------- /example/output/visualize/Input.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/Input.npz -------------------------------------------------------------------------------- /example/output/visualize/Input.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/Input.pdb -------------------------------------------------------------------------------- /example/output/visualize/Input.rinterface: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/Input.rinterface -------------------------------------------------------------------------------- /example/output/visualize/attention1.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/attention1.npy -------------------------------------------------------------------------------- /example/output/visualize/attention1_ligand.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/attention1_ligand.pdb -------------------------------------------------------------------------------- /example/output/visualize/attention1_receptor.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/attention1_receptor.pdb -------------------------------------------------------------------------------- /example/output/visualize/attention2.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/attention2.npy -------------------------------------------------------------------------------- /example/output/visualize/attention2_ligand.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/attention2_ligand.pdb -------------------------------------------------------------------------------- /example/output/visualize/attention2_receptor.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/example/output/visualize/attention2_receptor.pdb -------------------------------------------------------------------------------- /figure/attention.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/figure/attention.jpeg -------------------------------------------------------------------------------- /figure/network.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/figure/network.png -------------------------------------------------------------------------------- /figure/protocal.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/figure/protocal.jpeg -------------------------------------------------------------------------------- /main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/main.py -------------------------------------------------------------------------------- /model/GNN_Model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/model/GNN_Model.py -------------------------------------------------------------------------------- /model/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /model/layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/model/layers.py -------------------------------------------------------------------------------- /ops/Timer_Control.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/ops/Timer_Control.py -------------------------------------------------------------------------------- /ops/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/ops/__init__.py -------------------------------------------------------------------------------- /ops/argparser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/ops/argparser.py -------------------------------------------------------------------------------- /ops/os_operation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/ops/os_operation.py -------------------------------------------------------------------------------- /ops/train_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/ops/train_utils.py -------------------------------------------------------------------------------- /predict/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/predict/__init__.py -------------------------------------------------------------------------------- /predict/predict_multi_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/predict/predict_multi_input.py -------------------------------------------------------------------------------- /predict/predict_single_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/predict/predict_single_input.py -------------------------------------------------------------------------------- /predict/visualize_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/predict/visualize_attention.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kiharalab/GNN_DOVE/HEAD/requirements.txt --------------------------------------------------------------------------------