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molclaw-smiles-fg-editor

Edit SMILES strings to add, remove, or replace functional groups contextually.

28|2|Updated Mar 31, 2026
Search Tags:#validation#cheminformatics#smiles#functional-groups#molecule-editing#stereochemistry#smiles-parsing
One-click install
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-smiles-fg-editor
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molclaw-smiles-fg-editor
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-smiles-fg-editor
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-smiles-fg-editor

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Edit and modify molecular structures expressed as SMILES by adding, deleting, or replacing functional groups while avoiding common errors from naive substring matching and preserving stereochemistry and SMILES syntax.

Core Features & Use Cases

  • Context-aware functional group identification using a most-specific-to-least-specific hierarchy for oxygen- and nitrogen-containing groups.
  • Inventory, classify, filter, modify (add/delete/replace), and validate SMILES with preservation of stereochemical markers and checks for balanced parentheses and ring closures.
  • Use cases include requests like "delete hydroxyl", "add nitrile", or "replace amine with carboxyl" where the same SMILES pattern may represent different chemical groups depending on bonding context.

Quick Start

Replace the hydroxyl group in the SMILES CC(O)C with a nitrile and return the validated modified SMILES preserving stereochemistry.

Frequently Asked Questions about molclaw-smiles-fg-editor

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I replace functional groups in a SMILES string without breaking stereochemistry?▼

SMILES functional group editing identifies oxygen and nitrogen groups using a most-specific-to-least-specific classification hierarchy. This context-aware mechanism distinguishes chemical groups by bonding context, preventing errors from naive substring matching during molecular manipulation.

What is the best way to add a nitrile group to an existing SMILES molecule?▼

To delete a hydroxyl group from a SMILES string, apply context-aware molecule editing that targets the specific bonding context. The editor removes the functional group, validates syntax including parentheses and ring closures, and returns the modified SMILES in JSON format.

Why does naive substring matching fail when modifying SMILES functional groups?▼

SMILES functional group replacement handles amine-to-carboxyl substitutions by classifying nitrogen-containing groups hierarchically. The editor identifies the amine within its bonding context, replaces it with a carboxyl group, and validates the resulting SMILES syntax.

Can I use SMILES editing to disambiguate functional groups based on bonding context?▼

SMILES functional group editing preserves stereochemistry by retaining stereochemical markers during the add, delete, or replace operations. The editor also validates balanced parentheses and ring closures to ensure the modified SMILES string remains chemically valid.

Does SMILES molecule editing validate ring closures and parentheses after modifications?▼

SMILES molecule editing validates ring closures and parentheses after functional group modifications. The tool checks balanced parentheses and ring closures, preserves stereochemical markers, and returns the modified SMILES string in a simple JSON output format.

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