File size: 3,640 Bytes
83a9309 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | # --- 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")
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