organic-chemistry

name	organic-chemistry
description	Check if a SMARTS pattern matches a molecule using RDKit. Use when performing substructure matching on SMILES structures with SMARTS patterns, or checking functional groups in molecules.

Organic Chemistry: SMARTS Pattern Matching

Overview

Given a SMILES string and a SMARTS pattern, use RDKit to check if the molecule contains the functional group defined by the SMARTS pattern.

SMARTS Matching with RDKit

from rdkit import Chem

# Read input: SMILES on line 1, SMARTS on line 2
with open("/root/input.txt") as f:
    lines = f.read().strip().split("\n")
    smiles = lines[0].strip()
    smarts = lines[1].strip()

# Parse SMILES to molecule
mol = Chem.MolFromSmiles(smiles)
if mol is None:
    with open("/root/output.txt", "w") as f:
        f.write("Match: no\n")
    exit()

# Parse SMARTS to molecule pattern
pattern = Chem.MolFromSmarts(smarts)
if pattern is None:
    with open("/root/output.txt", "w") as f:
        f.write("Match: no\n")
    exit()

# Check if SMARTS matches the molecule
match = mol.HasSubstructMatch(pattern)

# Output
with open("/root/output.txt", "w") as f:
    f.write(f"Match: {'yes' if match else 'no'}\n")

Output Format

Match: yes

or

Match: no

Key Reference

• Chem.MolFromSmiles(smiles) — Parse SMILES string to molecule
• Chem.MolFromSmarts(smarts) — Parse SMARTS pattern to molecule pattern
• mol.HasSubstructMatch(pattern) — Returns True if pattern matches molecule
• Output "yes" if match exists, "no" otherwise