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#!/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())
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