| # --- Input Data Paths --- | |
| json_path: "../../my_protein.json" # User-defined | |
| pdb_filename: "../../heavy_chain.pdb" # User-defined | |
| torsion_info_path: "condensed_residues.json" # Assumed path - CHANGE IF DIFFERENT | |
| # --- Output Directories --- | |
| output_directories: | |
| checkpoint_dir: "checkpoints" # User-defined | |
| structure_dir: "structures" # User-defined | |
| latent_dir: "latent_reps" # User-defined | |
| # --- General Settings --- | |
| log_file: "my_logfile.log" # User-defined | |
| use_debug_logs: true # User-defined | |
| # force_cpu: false # Default: false (use GPU if available) | |
| # cuda_device: 0 # Default: 0 (first available GPU) | |
| num_workers: 4 # Default: 0 (can increase based on CPU cores) | |
| decoder_batch_size: 16 # User-defined (applied globally to decoders) | |
| inference_batch_size: 32 # Default: 32 (can adjust based on memory) | |
| # --- Model Hyperparameters --- | |
| knn_value: 4 # User-defined | |
| cheb_order: 4 # User-defined | |
| hidden_dim: 4 # User-defined (NOTE: This is very small!) | |
| pooling_dim_backbone: [22, 3] # User-defined | |
| pooling_dim_sidechain: [24, 3] # User-defined | |
| # --- HNO Encoder Training --- | |
| hno_training: | |
| hno_ckpt: "hno_model.pth" # Default filename | |
| batch_size: 16 # User-defined | |
| num_epochs: 400 # User-defined | |
| learning_rate: 0.0001 # User-defined | |
| save_interval: 10 # Default: 10 | |
| # --- Backbone Decoder Training --- | |
| decoderB_training: | |
| bb_decoder_ckpt: "decoder_backbone.pth" # Default filename | |
| num_epochs: 10 # User-defined (NOTE: This is very high!) | |
| learning_rate: 0.0001 # User-defined | |
| save_interval: 10 # User-defined | |
| decoder_depth: 3 # User-defined | |
| mlp_hidden_dim: 128 # Default: 128 (add if different needed) | |
| # Backbone Dihedral Loss Configuration (phi, psi) | |
| use_dihedral: true # User-defined | |
| lambda_1: 2.0 # User-defined (Weight for Divergence loss) | |
| lambda_2: 1.0 # User-defined (Weight for Torsion MSE loss) | |
| divergence_type: "KL" # Default: "KL" (Options: "KL", "JS", "Wasserstein") | |
| # --- Sidechain Decoder Training --- | |
| decoderSC_training: | |
| sc_decoder_ckpt: "decoder_sidechain.pth" # Default filename | |
| num_epochs: 10 # User-defined | |
| learning_rate: 1.0e-05 # User-defined (1e-5) | |
| save_interval: 10 # User-defined | |
| arch_type: 1 # Set to 1 based on user's 'stepB_use_zref: true' intent | |
| decoder_depth: 12 # User-defined | |
| mlp_hidden_dim: 128 # Default: 128 (add if different needed) | |
| # Sidechain Dihedral Loss Configuration (chi1-5) | |
| use_dihedral_sc: true # Default: false (Enable if desired) | |
| lambda_1_sc: 0.0 # Default: 0.0 (Weight for SC Divergence loss) | |
| lambda_2_sc: 0.0 # Default: 0.0 (Weight for SC Torsion MSE loss) | |
| divergence_type_sc: "KL" # Default: "KL" (Options: "KL", "JS", "Wasserstein") | |