# AbMelt Inference Pipeline Configuration
# Simulation parameters (for future use)
simulation:
  temperatures: [300, 350, 400]  # Kelvin
  simulation_time: 100           # nanoseconds
  force_field: "charmm27"        # or "charmm36-jul2022"
  water_model: "tip3p"
  salt_concentration: 150        # mM (PBS-like)
  gpu_enabled: true             # Set to true if using GPU acceleration
  pH: 7.4                        # pH for protonation state calculation
  p_salt: "NA"                   # Positive ion (NA+, K+, MG2+, CA2+)
  n_salt: "CL"                   # Negative ion (CL-)

# Input/Output paths
paths:
  run_dir: run_data/run_1/
  output_dir: "results"
  temp_dir: "temp"
  log_dir: "logs"

# Structure preparation settings
structure:
  validate_structure: true       # Validate PDB structure
  extract_sequences: true        # Extract chain sequences
  create_work_dir: true          # Create working directory

# GROMACS settings (for future preprocessing step)
gromacs:
  executable: "gmx"              # or "gmx_mpi" for MPI version
  config_dir: "config/gromacs"
  mdp_dir: "mdp"                 # Directory containing MDP template files
  n_threads: 8
  gpu_id: 0                      # GPU device ID (if using GPU)

# Logging
logging:
  level: "INFO"                  # DEBUG, INFO, WARNING, ERROR
  file: "logs/inference.log"
  max_size: "10MB"
  backup_count: 5

# Descriptor computation settings
descriptors:
  equilibration_time: 20 
  block_length: [2.5, 2.5]                # ns for order parameter blocks
  core_surface_k: 20             # number of residues for core/surface classification
  compute_lambda: true           # requires multiple temps, enabled for multi-temp runs

# Performance
performance:
  parallel_jobs: 4               # Number of parallel jobs (future use)
  cleanup_after: "inference"      # When to cleanup: "descriptors" (after descriptor computation) or "inference" (after predictions)
  delete_order_params: false     # If true, also delete order parameter CSV files (default: keep them for debugging)
  cleanup_temp: true             # Clean up temporary files after completion
  save_trajectories: false       # Save MD trajectories (large files)