multi_mcp/test_tools/chemistry/test_rdkit.py

"""
Test script for RDKit tools.

This script tests the functionality of the RDKit tools implemented in the
sci_mcp/chemistry_mcp/rdkit_tools module.
"""
import sys
import os

# Add the project root directory to the Python path
sys.path.append('/home/ubuntu/sas0/lzy/multi_mcp_server')

from sci_mcp.chemistry_mcp.rdkit_tools.rdkit_tools import (
    calculate_molecular_properties,
    calculate_drug_likeness,
    calculate_topological_descriptors,
    generate_molecular_fingerprints,
    calculate_molecular_similarity,
    analyze_molecular_structure,
    generate_molecular_conformer,
    identify_scaffolds,
    convert_between_chemical_formats,
    standardize_molecule,
    enumerate_stereoisomers,
    perform_substructure_search
)

def test_molecular_properties():
    """Test the calculation of molecular properties."""
    print("Testing calculate_molecular_properties...")
    # Aspirin
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    result = calculate_molecular_properties(smiles)
    print(result)
    print("-" * 80)

def test_drug_likeness():
    """Test the calculation of drug-likeness properties."""
    print("Testing calculate_drug_likeness...")
    # Aspirin
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    result = calculate_drug_likeness(smiles)
    print(result)
    print("-" * 80)

def test_topological_descriptors():
    """Test the calculation of topological descriptors."""
    print("Testing calculate_topological_descriptors...")
    # Aspirin
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    result = calculate_topological_descriptors(smiles)
    print(result)
    print("-" * 80)

def test_molecular_fingerprints():
    """Test the generation of molecular fingerprints."""
    print("Testing generate_molecular_fingerprints...")
    # Aspirin
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    result = generate_molecular_fingerprints(smiles, fingerprint_type="morgan")
    print(result)
    print("-" * 80)

def test_molecular_similarity():
    """Test the calculation of molecular similarity."""
    print("Testing calculate_molecular_similarity...")
    # Aspirin and Ibuprofen
    smiles1 = "CC(=O)OC1=CC=CC=C1C(=O)O"  # Aspirin
    smiles2 = "CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"  # Ibuprofen
    result = calculate_molecular_similarity(smiles1, smiles2)
    print(result)
    print("-" * 80)

def test_molecular_structure():
    """Test the analysis of molecular structure."""
    print("Testing analyze_molecular_structure...")
    # Aspirin
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    result = analyze_molecular_structure(smiles)
    print(result)
    print("-" * 80)

def test_molecular_conformer():
    """Test the generation of molecular conformers."""
    print("Testing generate_molecular_conformer...")
    # Aspirin
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    result = generate_molecular_conformer(smiles)
    print(result)
    print("-" * 80)

def test_scaffolds():
    """Test the identification of molecular scaffolds."""
    print("Testing identify_scaffolds...")
    # Aspirin
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    result = identify_scaffolds(smiles)
    print(result)
    print("-" * 80)

def test_format_conversion():
    """Test the conversion between chemical formats."""
    print("Testing convert_between_chemical_formats...")
    # Aspirin
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    result = convert_between_chemical_formats(smiles, "smiles", "inchi")
    print(result)
    print("-" * 80)

def test_standardize_molecule():
    """Test the standardization of molecules."""
    print("Testing standardize_molecule...")
    # Betaine with charges
    smiles = "C[N+](C)(C)CC(=O)[O-]"
    result = standardize_molecule(smiles)
    print(result)
    print("-" * 80)

def test_stereoisomers():
    """Test the enumeration of stereoisomers."""
    print("Testing enumerate_stereoisomers...")
    # 3-penten-2-ol (has both a stereocenter and a stereobond)
    smiles = "CC(O)C=CC"
    result = enumerate_stereoisomers(smiles)
    print(result)
    print("-" * 80)

def test_substructure_search():
    """Test the substructure search."""
    print("Testing perform_substructure_search...")
    # Aspirin, search for carboxylic acid group
    smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
    pattern = "C(=O)O"
    result = perform_substructure_search(smiles, pattern)
    print(result)
    print("-" * 80)

def main():
    """Run all tests."""
    print("Testing RDKit tools...\n")

    # Uncomment the tests you want to run
    test_molecular_properties()
    test_drug_likeness()
    test_topological_descriptors()
    test_molecular_fingerprints()
    test_molecular_similarity()
    test_molecular_structure()
    test_molecular_conformer()
    test_scaffolds()
    test_format_conversion()
    test_standardize_molecule()
    test_stereoisomers()
    test_substructure_search()

    print("All tests completed.")

if __name__ == "__main__":
    main()