Molecule Clipboard

🔗 Live app: https://ruibin-liu.github.io/molecule-clipboard/

Molecule Clipboard is a lightweight, browser‑based molecular tool combining JSME (for drawing and editing) and RDKit (for inspection and canonicalization) for SMILES, MOL, and SDF files.
It enables fast molecule drawing, editing, visualization, canonicalization, and physicochemical property calculation directly in the browser, with no installation and no data upload.

Runs locally · No uploads · Open source

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🔬 Overview

Molecule Clipboard is designed for chemists, cheminformaticians, and researchers who need a quick, reliable way to draw, edit, and inspect molecules without opening a notebook, setting up RDKit or JSME, or uploading proprietary structures to a server.

All computations are performed locally in the browser using RDKit.js, the official WebAssembly build of RDKit.

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✨ Key Features

• ✅ SMILES, MOL, and SDF input support
• ✅ Canonical SMILES, InChI, and InChIKey generation
• ✅ 2D SVG molecular structure rendering
• ✅ RDKit‑computed molecular descriptors:
  • Molecular weight (MW)
  • cLogP (Crippen)
  • TPSA
  • H‑bond donors / acceptors
  • Rotatable bonds
• ✅ Lipinski and Veber rule evaluation
• ✅ JSME molecular editor for drawing and editing structures
• ✅ Shareable URLs encoding molecular state
• ✅ Single‑file HTML application (portable and offline‑capable)

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🔐 Privacy & Security

• All computation runs locally in your browser
• No server‑side processing
• No uploads, logging, or tracking

This makes Molecule Clipboard suitable for confidential, proprietary, or unpublished molecular structures.

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🚀 Usage

Option 0 — Just click: https://ruibin-liu.github.io/molecule-clipboard/

Option 1 — Local

1. Download index.html
2. Open it in any modern browser (Chrome, Firefox, Safari)

Option 2 — Hosted

Host the file via GitHub Pages or any static web server.
Behavior and privacy guarantees remain identical.

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🧠 Typical Use Cases

• Sanity‑checking a copied SMILES string
• Converting molecular text into canonical representations
• Inspecting basic physicochemical properties
• Drawing and editing molecular structures with the integrated JSME editor
• Sharing molecules via URLs instead of files or screenshots
• Quick cheminformatics checks without a Python or RDKit environment

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🧩 Technology Stack

• RDKit.js (official minimal build)
• JSME (JavaScript Molecular Editor)
• WebAssembly (WASM)
• Pure HTML / CSS / JavaScript
• No build step or runtime dependencies

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⚠️ Limitations

• Intended for single‑molecule inspection, not batch processing
• Descriptor set limited to what is available in RDKit.js
• No 3D conformer generation or docking functionality

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📄 License

MIT License

This project is released under the MIT License to encourage reuse in both academic and industrial settings.

It uses the following third-party libraries:

• RDKit.js: BSD License - https://github.com/rdkit/rdkit-js
• JSME: BSD License - https://jsme-editor.github.io/

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📚 Citation

If you reference Molecule Clipboard in academic work, documentation, or supplementary material, please cite:

Molecule Clipboard — Browser‑based RDKit molecule inspection tool
https://github.com/Ruibin-Liu/molecule‑clipboard

Suggested BibTeX:

@software{molecule_clipboard,  
  title        = {Molecule Clipboard: Browser-Based RDKit Molecule Inspector},  
  author       = {Ruibin Liu},  
  year         = {2025},  
  url          = {https://github.com/Ruibin-Liu/molecule-clipboard},  
  note         = {Local, no-upload molecular inspection using RDKit.js}  
}