Molecular Substructure Validator

Build a molecular substructure validator that can identify specific structural patterns in chemical compounds and extract matching substructures.

Requirements

Your implementation should provide functionality to:

1. Pattern Detection: Check whether molecules contain specific structural patterns
2. Match Extraction: Find and return all instances of a pattern within a molecule
3. Multi-pattern Analysis: Analyze molecules against multiple patterns simultaneously

Specifications

Input Format

Your solution should accept molecules as SMILES strings (standard chemical notation format). For example:

• "CCO" represents ethanol
• "c1ccccc1" represents benzene
• "CC(=O)Oc1ccccc1C(=O)O" represents aspirin

Pattern Matching

Implement the ability to search for molecular patterns defined using specialized pattern notation. Your implementation should:

• Accept pattern definitions that specify structural features to match
• Return a boolean indicating pattern presence
• Extract all matching substructures when a pattern is found

Output Format

For pattern detection, return boolean values indicating presence/absence.

For match extraction, return a list of matches where each match is represented as a tuple of atom indices that participate in the substructure.

Test Cases

• Given a molecule with SMILES "CCO" and a hydroxyl pattern "[OH]", the validator detects the pattern is present @test
• Given aspirin "CC(=O)Oc1ccccc1C(=O)O" and a carboxylic acid pattern "C(=O)O", the validator extracts exactly two matches @test
• Given benzene "c1ccccc1" and an aromatic ring pattern "c1ccccc1", the validator confirms the pattern exists @test
• Given acetone "CC(=O)C" and a carbonyl pattern "C=O", the validator identifies one match with the correct atom indices @test

Implementation

@generates

API

def has_pattern(smiles: str, pattern: str) -> bool:
    """
    Check if a molecule contains a specific structural pattern.

    Args:
        smiles: SMILES string representation of the molecule
        pattern: Pattern definition to search for

    Returns:
        True if pattern is found, False otherwise
    """
    pass

def find_matches(smiles: str, pattern: str) -> list:
    """
    Find all instances of a pattern in a molecule.

    Args:
        smiles: SMILES string representation of the molecule
        pattern: Pattern definition to search for

    Returns:
        List of tuples, where each tuple contains atom indices of a match
    """
    pass

def analyze_patterns(smiles: str, patterns: dict) -> dict:
    """
    Analyze a molecule against multiple patterns.

    Args:
        smiles: SMILES string representation of the molecule
        patterns: Dictionary mapping pattern names to pattern definitions

    Returns:
        Dictionary mapping pattern names to their match counts
    """
    pass

Dependencies { .dependencies }

rdkit { .dependency }

Provides cheminformatics capabilities for molecular analysis.