File size: 4,514 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 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 | # General Settings
log_file: "logfile_multi_system.log" # Log file name
num_workers: 0 # Number of workers for DataLoader
force_cpu: false # Set to true to force CPU usage
cuda_device: 0 # GPU index if CUDA is available and force_cpu is false
# --- DATA INPUT CONFIGURATION (MODIFIED FOR MULTI-SYSTEM) ---
# Each entry in the 'systems' list represents one protein to be trained on.
data:
systems:
# --- System 1 ---
- pdb_path: "/scratch/asengar/long_sim/apo_d2_inv_start/run6/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_d2_inv_start/run6/residues_data.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_d2_inv_start/run6/condensed.json"
# --- System 2 ---
- pdb_path: "/scratch/asengar/long_sim/apo_d1/run1/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_d1/run1/residues_data_0.5.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_d1/run1/condensed.json"
# --- System 3 ---
- pdb_path: "/scratch/asengar/long_sim/apo_A2AR/run1/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_A2AR/run1/residues_data_0.1.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_A2AR/run1/condensed.json"
# --- System 4 ---
- pdb_path: "/scratch/asengar/long_sim/apo_beta1/run1/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_beta1/run1/residues_data_0.5.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_beta1/run1/condensed.json"
# --- System 5 ---
- pdb_path: "/scratch/asengar/long_sim/apo_M1/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_M1/residues_data.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_M1/condensed.json"
# --- System 6 ---
- pdb_path: "/scratch/asengar/long_sim/apo_H1/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_H1/residues_data.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_H1/condensed.json"
# --- System 7 ---
- pdb_path: "/scratch/asengar/long_sim/apo_d3/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_d3/residues_data.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_d3/condensed.json"
# --- System 8 ---
- pdb_path: "/scratch/asengar/long_sim/apo_beta2/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_beta2/residues_data.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_beta2/condensed.json"
# --- System 9 ---
- pdb_path: "/scratch/asengar/long_sim/apo_h5t2a/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_h5t2a/residues_data.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_h5t2a/condensed.json"
# --- System 10 ---
- pdb_path: "/scratch/asengar/long_sim/apo_5ht1b/heavy_chain.pdb"
json_path: "/scratch/asengar/long_sim/apo_5ht1b/residues_data.json"
torsion_info_path: "/scratch/asengar/long_sim/apo_5ht1b/condensed.json"
# Graph Construction Settings
graph:
knn_value: 4 # K for k-NN graph construction
# --- GLOBAL MODEL & TRAINING SETTINGS ---
# These settings apply to the single, shared models trained on all systems.
hno_encoder:
hidden_dim: 16
cheb_order: 4
num_epochs: 5
learning_rate: 0.0001
batch_size: 16
save_interval: 50
decoder2:
num_epochs: 10
learning_rate: 0.0003
batch_size: 16
base_loss_weight: 1.0
save_interval: 500
use_z_ref_ensemble: false
decoder2_settings:
conditioner_mode: "z_ref" # Must be 'z_ref' for the multi-system code
mlp_hidden_dim: 16
num_hidden_layers: 12
# NOTE: pooling_type, output_height/width are no longer used by the new decoder
pooling_type: "blind"
output_height: 50
output_width: 2
# Dihedral Loss Configuration (Global Weights)
dihedral_loss:
# This is a global switch. Set to true to attempt using dihedral loss.
use_dihedral_loss: false
# The specific torsion_info_path is now defined per-system above.
lambda_divergence: 0.1
lambda_torsion_mse: 1.0
divergence_type: "JS"
# Data Augmentation Settings
data_augmentation:
enabled: true
ensemble_size: 50
target_ca_rmsd: 1.0
# Structural Augmentation Settings
structural_augmentation:
enabled: true
variants_per_system: 10
# Execution Settings
execution_settings:
limit_systems: 2
max_frames_per_system: 500
# Output Directories Configuration
output_directories:
checkpoint_dir: "checkpoints"
structure_dir: "structures"
latent_dir: "latent_reps"
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