Prediction Examples

1. Data Preprocessing

python ./access/data/data_prepare.py \
  --pdb_dir ./rosetta/pdb_rosetta \          # Input directory for original PDB files
  --include_dir ./PDB_file \                 # Directory for specific PDB files to include
  --embedding_dir ./access/gvp_protein_embedding \  # Output directory for GVP embeddings
  --processed_dir ./access/gvp_protein_embedding/processed \  # Directory for preprocessed data
  --label_file train_labels_all_0001.csv  # Prediction file

2. Model Prediction

python ./access/inference/inference.py \
  --model ./access/saved_models/best_model.pt \
  --root_dir ./access/gvp_protein_embedding/processed \
  --resultFolder ./access/result \
  --print_embedding

3. Output Results

protein_name	pred_label	key_residues
AF-P00780-F1-model_v4_0001	3.4.21.62/0.3088	170, 324, 229, 146, 171, 200, 227, 230, 138, 326, 137, 328, 167, 173, 198, 196, 330, 164, 256, 142, 141, 169, 168, 140, 139, 323, 329, 172, 325, 304, 279, 166, 284, 305, 165, 231, 163, 261
AF-A0A0K8P6T7-F1-model_v4_0001	3.1.1.101/0.3083	85, 162, 158, 254, 163, 86, 202, 164, 159, 160, 118, 237, 161, 82, 166, 186, 184, 214, 165, 156, 183, 182, 181, 87, 157, 240, 123, 88, 120
AF-P11797-F1-model_v4_0001	3.2.1.14/0.3240	290, 182, 95, 211, 380, 144, 403, 185, 305, 402, 292, 294, 214, 142, 407, 288, 187, 124, 188, 140, 93, 10, 269, 186, 404, 96, 291, 141, 212, 270, 53, 217, 228, 289, 268, 374, 184, 143, 215, 295, 408, 210, 213, 183, 97, 227, 379, 389, 98, 94