infer.py

import sys
import logging
import yaml
from pathlib import Path
import argparse

# Add src to path for imports
sys.path.append(str(Path(__file__).parent / "src"))

from structure_prep import prepare_structure, load_existing_structure_files
from md_simulation import run_md_simulation, load_existing_simulation_results
from compute_descriptors import compute_descriptors, load_existing_descriptors
from model_inference import run_model_inference, load_existing_predictions
from cleanup_temp_files import cleanup_temp_directory
from timing import get_timing_report, reset_timing_report, time_step

def main():
    # Parse command line arguments
    parser = argparse.ArgumentParser(description='AbMelt Inference Pipeline')
    
    # Input options - either sequences or PDB file
    input_group = parser.add_mutually_exclusive_group(required=True)
    input_group.add_argument('--h', '--heavy', type=str, 
                           help='Heavy chain amino acid sequence (use with --l)')
    input_group.add_argument('--pdb', type=str,
                           help='Input PDB file path')
    
    parser.add_argument('--l', '--light', type=str,
                       help='Light chain amino acid sequence (use with --h)')
    parser.add_argument('--name', type=str, default='antibody',
                       help='Antibody name/identifier')
    parser.add_argument('--config', type=str,
                       help='Configuration file path')
    parser.add_argument('--output', type=str, default='results',
                       help='Output directory')
    
    # Skip step flags
    parser.add_argument('--skip-structure', action='store_true',
                       help='Skip structure preparation step (load existing files)')
    parser.add_argument('--skip-md', action='store_true',
                       help='Skip MD simulation step (load existing trajectory files)')
    parser.add_argument('--skip-descriptors', action='store_true',
                       help='Skip descriptor computation step (load existing descriptors)')
    parser.add_argument('--skip-inference', action='store_true',
                       help='Skip model inference step (load existing predictions)')
    
    # Timing options
    parser.add_argument('--timing-report', type=str, metavar='PATH',
                       help='Save timing report to JSON file (also prints summary to console)')
    
    args = parser.parse_args()
    
    # Validate arguments
    if args.h and not args.l:
        parser.error("--l/--light is required when using --h/--heavy")
    if args.l and not args.h:
        parser.error("--h/--heavy is required when using --l/--light")
    
    # 1. Load configuration
    config = load_config(args.config)
    
    # 2. Setup logging and directories
    setup_logging(config)
    create_directories(config)

    # Initialize timing report
    reset_timing_report()
    timing_report = get_timing_report()
    timing_report.start()

    # 3. Create antibody input based on input type
    if args.pdb:
        # Input from PDB file
        antibody = {
            "name": args.name,
            "pdb_file": args.pdb,
            "type": "pdb"
        }
    else:
        # Input from sequences
        antibody = {
            "name": args.name,
            "heavy_chain": args.h,
            "light_chain": args.l,
            "type": "sequences"
        }
    
    # 4. Run inference pipeline
    try:
        result = run_inference_pipeline(
            antibody, 
            config,
            skip_structure=args.skip_structure,
            skip_md=args.skip_md,
            skip_descriptors=args.skip_descriptors,
            skip_inference=args.skip_inference
        )
        
        print(f"Inference pipeline for {args.name}:")
        print(f"  Status: {result['status']}")
        print(f"  Message: {result['message']}")
        print(f"  PDB file: {result['structure_files']['pdb_file']}")
        print(f"  Work directory: {result['structure_files']['work_dir']}")
        
        if 'chains' in result['structure_files']:
            print(f"  Chains found: {list(result['structure_files']['chains'].keys())}")
        
        if 'simulation_result' in result:
            print(f"  MD simulations completed at temperatures: {list(result['simulation_result']['trajectory_files'].keys())}")
            for temp, files in result['simulation_result']['trajectory_files'].items():
                print(f"    {temp}K: {files['final_xtc']}")
        
        if 'descriptor_result' in result:
            print(f"  Descriptors computed: {result['descriptor_result']['descriptors_df'].shape[1]} features")
            print(f"  XVG files generated: {len(result['descriptor_result']['xvg_files'])}")
        
        if 'inference_result' in result:
            print(f"\n=== PREDICTIONS ===")
            predictions = result['inference_result']['predictions']
            for model_name, pred in predictions.items():
                if pred is not None:
                    print(f"  {model_name.upper()}: {pred[0]:.3f}")
                else:
                    print(f"  {model_name.upper()}: FAILED")
        
        # Add timing data to result
        result['timing'] = timing_report.to_dict()
        
    finally:
        # Stop timing - always runs even on exception
        timing_report.stop()
        
        # Print timing report - always runs even on exception
        print(timing_report.format_summary())
        
        # Save timing report if requested - always runs even on exception
        if args.timing_report:
            timing_report.save_json(args.timing_report)
            print(f"\nTiming report saved to: {args.timing_report}")
    
    return result
    


def load_config(config_path: str) -> dict:
    """Load configuration from YAML file."""
    try:
        with open(config_path, 'r') as f:
            config = yaml.safe_load(f)
        return config
    except Exception as e:
        raise Exception(f"Failed to load config: {e}")

def setup_logging(config: dict):
    """Setup logging configuration."""
    log_level = getattr(logging, config["logging"]["level"].upper())
    log_file = config["logging"]["file"]
    
    # Create log directory if it doesn't exist
    Path(log_file).parent.mkdir(parents=True, exist_ok=True)
    
    logging.basicConfig(
        level=log_level,
        format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
        handlers=[
            logging.FileHandler(log_file),
            logging.StreamHandler(sys.stdout)
        ]
    )


def create_directories(config: dict):
    """Create necessary directories."""
    script_directory = Path(__file__).parent.resolve()
    config['paths']['output_dir'] = script_directory / config["paths"]["run_dir"] / config['paths']['output_dir']
    config['paths']['temp_dir'] = script_directory / config["paths"]["run_dir"] / config['paths']['temp_dir']
    config['paths']['log_dir'] = script_directory / config["paths"]["run_dir"] / config['paths']['log_dir']

    directories = [
        config["paths"]["output_dir"],
        config["paths"]["temp_dir"],
        config["paths"]["log_dir"]
    ]
    
    for directory in directories:
        Path(directory).mkdir(parents=True, exist_ok=True)


def run_inference_pipeline(antibody, config, skip_structure=False, skip_md=False, skip_descriptors=False, skip_inference=False):
    """

    Run the complete inference pipeline.

    

    Args:

        antibody: Dictionary containing antibody information

        config: Configuration dictionary

        skip_structure: If True, load existing structure files instead of preparing

        skip_md: If True, load existing MD simulation results instead of running

        skip_descriptors: If True, load existing descriptors instead of computing

        skip_inference: If True, load existing predictions instead of computing

        

    Returns:

        Dictionary containing pipeline results

    """
    logging.info(f"Starting inference pipeline for antibody: {antibody['name']}")
    
    if skip_structure:
        logging.info("Skipping structure preparation (using --skip-structure flag)")
    if skip_md:
        logging.info("Skipping MD simulation (using --skip-md flag)")
    if skip_descriptors:
        logging.info("Skipping descriptor computation (using --skip-descriptors flag)")
    if skip_inference:
        logging.info("Skipping model inference (using --skip-inference flag)")
    
    try:
        # Step 1: Structure preparation
        with time_step("Structure Preparation"):
            if skip_structure:
                logging.info("Step 1: Loading existing structure files...")
                structure_files = load_existing_structure_files(antibody, config)
                logging.info("Structure files loaded successfully")
            else:
                logging.info("Step 1: Preparing structure...")
                structure_files = prepare_structure(antibody, config)
                logging.info("Structure preparation completed")
        
        # Log structure files
        logging.info(f"Structure files:")
        for key, path in structure_files.items():
            if key != "chains":
                logging.info(f"  {key}: {path}")
        
        if "chains" in structure_files:
            logging.info(f"  chains: {list(structure_files['chains'].keys())}")
        
        # Step 2: MD simulation
        with time_step("MD Simulation"):
            if skip_md:
                logging.info("Step 2: Loading existing MD simulation results...")
                simulation_result = load_existing_simulation_results(structure_files, config)
                logging.info("MD simulation results loaded successfully")
            else:
                logging.info("Step 2: Running MD simulations...")
                simulation_result = run_md_simulation(structure_files, config)
                logging.info("MD simulations completed")
        
        # Log trajectory files
        logging.info(f"Trajectory files:")
        for temp, files in simulation_result["trajectory_files"].items():
            logging.info(f"  {temp}K: {files['final_xtc']}")
        
        # Step 3: Descriptor computation
        with time_step("Descriptor Computation"):
            if skip_descriptors:
                logging.info("Step 3: Loading existing descriptor computation results...")
                descriptor_result = load_existing_descriptors(simulation_result, config)
                logging.info("Descriptor computation results loaded successfully")
            else:
                logging.info("Step 3: Computing descriptors...")
                descriptor_result = compute_descriptors(simulation_result, config)
                logging.info("Descriptor computation completed")
        
        # Log descriptor computation results
        logging.info(f"Descriptors:")
        logging.info(f"  DataFrame shape: {descriptor_result['descriptors_df'].shape}")
        logging.info(f"  Number of features: {len(descriptor_result['descriptors_df'].columns)}")
        logging.info(f"  XVG files: {len(descriptor_result['xvg_files'])}")
        
        # Step 4: Model inference
        with time_step("Model Inference"):
            if skip_inference:
                logging.info("Step 4: Loading existing model predictions...")
                work_dir = Path(descriptor_result['work_dir'])
                inference_result = load_existing_predictions(work_dir, antibody['name'])
                logging.info("Model predictions loaded successfully")
            else:
                logging.info("Step 4: Running model inference...")
                inference_result = run_model_inference(descriptor_result, config)
                logging.info("Model inference completed")
        
        # Log prediction results
        logging.info(f"Predictions:")
        for model_name, pred in inference_result['predictions'].items():
            if pred is not None:
                logging.info(f"  {model_name}: {pred[0]:.3f}")
            else:
                logging.info(f"  {model_name}: FAILED")
        
        # Cleanup intermediate files if configured
        cleanup_config = config.get("performance", {})
        if cleanup_config.get("cleanup_temp", False):
            cleanup_after = cleanup_config.get("cleanup_after", "inference")
            if cleanup_after == "inference":
                logging.info("Cleaning up intermediate files...")
                try:
                    temperatures = [str(t) for t in config["simulation"]["temperatures"]]
                    cleanup_stats = cleanup_temp_directory(
                        work_dir=Path(descriptor_result['work_dir']),
                        antibody_name=antibody['name'],
                        temperatures=temperatures,
                        dry_run=False,
                        keep_order_params=not cleanup_config.get("delete_order_params", False)
                    )
                    logging.info(f"Cleanup completed: deleted {cleanup_stats.get('deleted', 0)} files")
                except Exception as e:
                    logging.warning(f"Cleanup failed (non-fatal): {e}")
        
        result = {
            "status": "success",
            "structure_files": structure_files,
            "simulation_result": simulation_result,
            "descriptor_result": descriptor_result,
            "inference_result": inference_result,
            "message": "Complete inference pipeline finished successfully."
        }
        
        logging.info("Inference pipeline completed successfully")
        return result
        
    except Exception as e:
        logging.error(f"Inference pipeline failed: {e}")
        raise


if __name__ == "__main__":
    main()