tests/simple_structure_test.py

#!/usr/bin/env python3

"""
Simple test script for AbMelt structure generation.
Quick test to verify structure generation functionality works.
"""

import os
import sys
import logging
from pathlib import Path

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

# Setup basic logging
logging.basicConfig(level=logging.INFO, format='%(levelname)s: %(message)s')
logger = logging.getLogger(__name__)

def test_imports():
    """Test that all required modules can be imported."""
    logger.info("Testing imports...")
    
    try:
        from structure_prep import (
            prepare_structure, 
            generate_structure_from_sequences,
            validate_structure,
            get_chain_sequences
        )
        logger.info("✓ Successfully imported structure_prep modules")
        return True
    except ImportError as e:
        logger.error(f"✗ Failed to import structure_prep modules: {e}")
        return False

def test_immune_builder():
    """Test ImmuneBuilder functionality."""
    logger.info("Testing ImmuneBuilder...")
    
    try:
        from structure_prep import generate_structure_from_sequences
        
        # Test sequences (shortened for testing)
        heavy_chain = "QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYWMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATITADESTSTTAYMELSSLRSEDTAVYYCARGGYSSGYYFDYWGQGTLVTVSS"
        light_chain = "DIQMTQSPSSLSASVGDRVTITCRASQDISNYLNWFQQKPGKAPKLLIYYATSLADGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQGNTFPWTFGQGTKVEIKR"
        
        # Generate structure
        output_file = "test_antibody.pdb"
        generated_file = generate_structure_from_sequences(
            heavy_chain=heavy_chain,
            light_chain=light_chain,
            output_file=output_file
        )
        
        # Check if file was created
        if Path(generated_file).exists():
            logger.info(f"✓ ImmuneBuilder generated structure: {generated_file}")
            
            # Test validation
            is_valid = validate_structure(generated_file)
            if is_valid:
                logger.info("✓ Structure validation passed")
            else:
                logger.warning("⚠ Structure validation failed")
            
            # Test sequence extraction
            chains = get_chain_sequences(generated_file)
            if chains:
                logger.info(f"✓ Extracted chains: {list(chains.keys())}")
            else:
                logger.warning("⚠ Failed to extract chain sequences")
            
            # Cleanup
            Path(generated_file).unlink()
            logger.info("✓ Cleaned up test file")
            
            return True
        else:
            logger.error(f"✗ ImmuneBuilder failed to generate structure")
            return False
            
    except Exception as e:
        logger.error(f"✗ ImmuneBuilder test failed: {e}")
        return False

def test_prepare_structure():
    """Test the main prepare_structure function."""
    logger.info("Testing prepare_structure function...")
    
    try:
        from structure_prep import prepare_structure
        
        # Test configuration
        config = {
            "paths": {
                "temp_dir": "test_temp",
                "output_dir": "test_output",
                "log_dir": "test_logs"
            }
        }
        
        # Create test directories
        for path in config["paths"].values():
            Path(path).mkdir(parents=True, exist_ok=True)
        
        # Test antibody data
        antibody = {
            "name": "test_antibody",
            "heavy_chain": "QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYWMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATITADESTSTTAYMELSSLRSEDTAVYYCARGGYSSGYYFDYWGQGTLVTVSS",
            "light_chain": "DIQMTQSPSSLSASVGDRVTITCRASQDISNYLNWFQQKPGKAPKLLIYYATSLADGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQGNTFPWTFGQGTKVEIKR",
            "type": "sequences"
        }
        
        # Run prepare_structure
        structure_files = prepare_structure(antibody, config)
        
        # Verify results
        required_keys = ["pdb_file", "work_dir", "chains"]
        for key in required_keys:
            if key not in structure_files:
                logger.error(f"✗ Missing required key: {key}")
                return False
        
        # Check if files exist
        pdb_file = Path(structure_files["pdb_file"])
        work_dir = Path(structure_files["work_dir"])
        
        if not pdb_file.exists():
            logger.error(f"✗ PDB file does not exist: {pdb_file}")
            return False
        
        if not work_dir.exists():
            logger.error(f"✗ Work directory does not exist: {work_dir}")
            return False
        
        logger.info(f"✓ prepare_structure successful")
        logger.info(f"  PDB file: {pdb_file}")
        logger.info(f"  Work dir: {work_dir}")
        logger.info(f"  Chains: {list(structure_files['chains'].keys())}")
        
        # Cleanup
        import shutil
        shutil.rmtree("test_temp")
        shutil.rmtree("test_output")
        shutil.rmtree("test_logs")
        logger.info("✓ Cleaned up test directories")
        
        return True
        
    except Exception as e:
        logger.error(f"✗ prepare_structure test failed: {e}")
        return False

def main():
    """Run all tests."""
    logger.info("=" * 50)
    logger.info("ABMELT STRUCTURE GENERATION TEST")
    logger.info("=" * 50)
    
    tests = [
        ("Import Test", test_imports),
        ("ImmuneBuilder Test", test_immune_builder),
        ("Prepare Structure Test", test_prepare_structure)
    ]
    
    results = []
    
    for test_name, test_func in tests:
        logger.info(f"\n{test_name}:")
        try:
            result = test_func()
            results.append((test_name, result))
        except Exception as e:
            logger.error(f"✗ {test_name} failed with exception: {e}")
            results.append((test_name, False))
    
    # Summary
    logger.info("\n" + "=" * 50)
    logger.info("TEST SUMMARY")
    logger.info("=" * 50)
    
    passed = sum(1 for _, result in results if result)
    total = len(results)
    
    for test_name, result in results:
        status = "✓ PASS" if result else "✗ FAIL"
        logger.info(f"{test_name}: {status}")
    
    logger.info(f"\nOverall: {passed}/{total} tests passed")
    
    if passed == total:
        logger.info("🎉 All tests passed!")
        return 0
    else:
        logger.error("❌ Some tests failed")
        return 1

if __name__ == "__main__":
    sys.exit(main())