SELFIES Language Extension for VS Code

See your molecules as you write them.

Define molecular fragments, compose them into complex structures, and watch the visualization update live as you navigate your code.

Why SELFIES?

SELFIES was designed for machine learning — every string is a valid molecule, eliminating syntax errors in generative models. The DSL extends that principle: named fragments are easier for LLMs to compose correctly than raw atom strings, and undefined references fail loudly instead of producing silent errors.

The Problem

Pharmaceutical SMILES are write-only:

CC(=O)Nc1ccc(O)cc1

And when LLMs generate SMILES, they hallucinate invalid structures. SELFIES fixes the validity problem. The DSL fixes the readability problem.

With this extension, you write readable, composable definitions:

[acetyl] = [methyl][carbonyl]
[acetamide] = [acetyl][amino]
[acetaminophen] = [acetamide][para_hydroxyphenyl]

And see the structure instantly — formula, weight, 2D rendering — as your cursor moves through the file.

Installation

Install from VS Code Marketplace

Or search "SELFIES" in the VS Code extensions panel.

Quick Start

1. Create a file with .selfies extension
2. Start defining molecules — the preview panel opens automatically
3. Move your cursor to any definition to see its structure

# fragments.selfies
[methyl] = [C]
[ethyl] = [C][C]
[hydroxyl] = [O]

[ethanol] = [ethyl][hydroxyl]
[methanol] = [methyl][hydroxyl]

Features

Live Preview

As your cursor moves, the preview panel shows:

• 2D molecular structure
• Molecular formula
• Molecular weight
• SMILES output
• Export as SVG or PNG

Syntax Highlighting

Full highlighting for atoms, bonds, branches, rings, comments, and references.

Real-time Diagnostics

Instant feedback on:

• Undefined references
• Circular dependencies
• Duplicate definitions
• Syntax errors

Multi-file Projects

Import fragments across files:

import "./fragments.selfies"                       # import all
import [methyl, ethyl] from "./fragments.selfies"  # import specific

Commands

• SELFIES: Show Molecular Structure — Open the preview panel
• SELFIES: Toggle Preview Panel — Toggle preview on/off

Settings

Language Rules

• No forward references — Define before you use
• No recursion — No circular dependencies
• Single assignment — No redefinitions
• Case sensitive — [Methyl] ≠ [methyl]

Related

• selfies-js — The underlying library (also usable as CLI and npm package)
• SELFIES paper — Original research by the Aspuru-Guzik group

Citation

If you use SELFIES in your research:

Krenn, M., Häse, F., Nigam, A., Friederich, P., & Aspuru-Guzik, A. (2020). Self-referencing embedded strings (SELFIES): A 100% robust molecular string representation. Machine Learning: Science and Technology, 1(4), 045024.

License

MIT