xushuwenn/redact/organic-chemistry-smarts

Claude Code and agent skill by xushuwenn/redact

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Match SMILES molecules against SMARTS patterns to detect functional groups using RDKit.

Install

npx vskill@latest install xushuwenn/redact/organic-chemistry-smarts

SKILL.md

SMARTS Pattern Matching for Molecules

When to Use

  • Check if molecules contain specific functional groups
  • Use SMARTS patterns for substructure search
  • Detect chemical features via pattern matching

Input Format

File /root/input.txt (2 lines):

  • Line 1: SMILES string
  • Line 2: SMARTS pattern

Output Format

To /root/output.txt:

Match: yes/no

Output "yes" if pattern matches, "no" otherwise.

Using RDKit

python
from rdkit import Chem
mol = Chem.MolFromSmiles(smiles)
pattern = Chem.MolFromSmarts(smarts_pattern)
if mol.HasSubstructMatch(pattern):
    # Match found

SMARTS Patterns

  • Common patterns for functional groups
  • Use RDKit's SMARTS support for matching
  • Handle aromatic and aliphatic variants

Tips

  • Parse SMILES and SMARTS from input file
  • Use HasSubstructMatch for checking
  • Handle invalid patterns gracefully

Security

  • Security scanPassed, 90 of 100Pattern checks on the skill's files.
  • Model reviewPassed

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Quality evaluation

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Source

Popularity

Repository stars
13
7-day trend score
18

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