molecules.js

A JavaScript cheminformatics library with an interactive demo for editing and analyzing molecular structures.

Open the demo →

Quick start

Documentation

Structure editing and analysis

• Load SMILES, InChI, or molecules from the built-in catalog.
• Draw atoms, bonds, chains, and rings; edit charges and stereobonds; undo and redo.
• Inspect topological indices, logP, TPSA, hydrogen bonding, Lipinski rules, and approximate QED.
• Highlight functional groups and supported descriptor contributions.
• Style structures, copy SVG/PNG, and save or reopen molecule JSON.

Force-directed graphs

Switch between skeletal 2D structures and force-directed graphs. Both views support pan, zoom, rotation, and atom selection.

Reactions and resonance

Preview SMIRKS reaction templates with reagent and condition annotations. Enumerate resonance contributors and inspect electron-flow arrows. Additional overlays show electronegativity, bond lengths, and atom numbering.

Library capabilities

• Formats: SMILES, canonical SMILES, InChI, JSON, and sequence-to-molecule utilities.
• Matching: SMARTS, VF2 subgraph search, aromaticity perception, and Morgan ranking.
• Transformations: atom-mapped SMIRKS, reaction templates, and resonance enumeration.
• 2D layout: generation and refinement for chains, fused/spiro/bridged rings, macrocycles, and organometallic structures; deterministic cleanup by default.
• Analysis: graph matrices, topological and spectral descriptors, physicochemical estimates, and valence validation.

Quick start

Requires Node.js 24.15+. Use a checkout of this repository. The npm package named molecules is an unrelated project.

git clone https://github.com/chemplexity/molecules.git
cd molecules
npm install

Save this as example.mjs in the repository root and run node example.mjs:

import { parseSMILES, generateCoords, tpsa, findSMARTS } from './src/index.js';

const aspirin = parseSMILES('CC(=O)Oc1ccccc1C(=O)O');
generateCoords(aspirin);

console.log(tpsa(aspirin)); // 63.6 Ų
console.log([...findSMARTS(aspirin, '[CX3](=O)[OX2H1]')].length); // 1

The library uses ESM and declares no runtime npm dependencies. npm run build generates shared ESM modules in es/ and standalone bundles in dist/; the example above runs directly from source.

Run the demo locally

From a checkout of this repository:

npm install
node tests/e2e/server.mjs

Open http://127.0.0.1:4173. No build step required; the demo loads D3 7.9.0 from jsDelivr.