#MoonSMILES - A Molecular Processing Library for MoonBit

#Key Features

#SMILES String Processing

• Validation & Parsing: Validate SMILES string correctness, check bracket balance, and parse into internal molecular representation
• Normalization & Standardization: Clean SMILES strings and generate canonical forms to ensure consistent representation
• Format Conversion: Convert between SMILES strings and molecular structure objects

#Molecular Structure Analysis

• Atom & Bond Counting: Calculate the number of atoms and bonds in molecules
• Ring Structure Detection: Find all ring structures and distinguish between aromatic and non-aromatic rings
• Substructure Searching: Detect specific structural patterns within molecules
• Formula Generation: Generate molecular formulas (like C2H6O) from structure

#Drug Property Analysis

• Molecular Weight Calculation: Compute exact mass of molecules
• LogP Prediction: Estimate octanol-water partition coefficient (lipophilicity/hydrophilicity indicator)
• Lipinski Rule Checking: Evaluate drug-likeness of molecules
• Hydrogen Bond Properties: Calculate hydrogen bond donors and acceptors
• Rotatable Bond Counting: Analyze molecular flexibility

#Molecular Similarity Comparison

• Molecular Fingerprint Generation: Create bit vectors representing molecular structural features
• Similarity Calculation: Compare structural similarity between molecules using Tanimoto coefficient

#Usage Examples

#Basic SMILES Processing

test {
    // Validate SMILES string
    let is_valid = validate_smiles("C=C(C)O")  // true
    assert_eq(is_valid, true)
}

test {
    // Normalization
    let normalized_result = normalize_smiles("C = C ( C ) O")  // returns Result[String, String]
    let normalized = normalized_result.unwrap()  // or use match if .unwrap() is not available
    assert_eq(normalized, "C=C(C)O")
}

test {
    // Parse into molecular structure
    let molecule = parse_smiles("CCO")  // ethanol
    assert_eq(molecule.atoms.length(), 3)
}

test {
    // Generate canonical SMILES
    let molecule = parse_smiles("CCO")
    let canonical = generate_canonical_smiles(molecule)
    assert_eq(canonical, "CCO")
}

#Molecular Property Calculation

test {
    // Calculate molecular weight
    let molecule = parse_smiles("CCO")
    let mol_weight = calculate_molecular_weight(molecule)  // ~46.07 g/mol
    assert_eq(mol_weight > 46.0 && mol_weight < 46.1, true)
}

test {
    // Calculate LogP value (partition coefficient)
    let molecule = parse_smiles("CCO")
    let logp = calculate_logp(molecule)  // negative value indicates hydrophilicity
    assert_eq(logp < 0.0, true)
}

test {
    // Check drug-likeness
    let molecule = parse_smiles("CCO")
    let (passes_lipinski, _) = check_lipinski_rule_of_five(molecule)
    assert_eq(passes_lipinski, true)
}

test {
    // Count rotatable bonds
    let molecule = parse_smiles("CCO")
    let rotatable_bonds = count_rotatable_bonds(molecule)
    assert_eq(rotatable_bonds, 1)
}

#Structure Analysis

test {
    // Find all rings
    let molecule = parse_smiles("c1ccccc1")  // benzene
    let rings = find_all_rings(molecule)
    assert_eq(rings.length(), 1)
}

test {
    // Identify aromatic rings
    let molecule = parse_smiles("c1ccccc1")  // benzene
    let aromatic_rings = identify_aromatic_rings(molecule)
    assert_eq(aromatic_rings.length(), 1)
}

test {
    // Check for specific substructures
    let molecule = parse_smiles("CCO")
    let has_hydroxyl = contains_substructure(molecule, "O")  // check for hydroxyl group
    assert_eq(has_hydroxyl, true)
}

#Molecular Similarity

test {
    // Calculate similarity between two molecules
    let mol1 = parse_smiles("CCO")
    let mol2 = parse_smiles("CCC")
    let similarity = calculate_similarity(mol1, mol2)
    assert_eq(similarity > 0.4, true)
}

test {
    // Calculate similarity directly from SMILES
    let smiles_similarity = calculate_smiles_similarity("CCO", "CCC")
    assert_eq(smiles_similarity > 0.4, true)
}

#Special Features

• Support for extended atom representations including isotope labeling and charge states: [13CH3], [NH4+]
• Support for aromaticity representation: c1ccccc1 (benzene)
• Handling of complex ring structures and multi-ring systems

#Application Domains

• Drug discovery and design
• Compound screening and virtual screening
• Chemical database searching
• Structure-activity relationship (SAR) studies
• Chemical education and research