AtomLens

What it does

• Open chemistry formats such as MOL, SDF, SMILES, InChI, MOL2, PDB, XYZ, CML, RXN, and RDF.
• Render 2D molecular depictions in a native macOS interface.
• Generate identifiers: SMILES, isomeric SMILES, InChI, and InChI Key.
• Calculate core properties like formula, molecular weight, monoisotopic mass, LogP, and Rule-of-Five status.
• Search molecule files locally through Spotlight metadata and preview with Quick Look.

Tip: The Help page includes practical search queries and full format tables.

Designed for local workflows

AtomLens is built for day-to-day lab and research work where fast file triage and reliable local processing matter. You can inspect structures, export in common formats, and keep all data on your Mac.

Try sample structures

Use this starter set of molecule files to test parsing, rendering, and Spotlight/Quick Look workflows in AtomLens.

Download example structures (ZIP, 90 KB)

Stable link for future site updates: /assets/downloads/atomlens-example-structures.zip

Screenshots

The spark: why this app exists

If you work with molecules, you know the moment: someone sends "the compound" as an SDF attachment, your downloads folder becomes a museum, and a week later you remember it had an InChI Key — but not the filename. Traditional cheminformatics tools are powerful, but the operating system itself still treats molecule files like anonymous text.

AtomLens started as a simple wish: "Finder should be able to preview and search molecules like it previews and searches PDFs." From that, a surprisingly ambitious requirements list fell out:

• Open common chemistry formats: SDF, MOL, SMILES, InChI, and more.
• Render chemist-friendly 2D depictions: aromatic rings read as aromatic, chains are readable, stereo bonds are unambiguous.
• Compute identifiers and properties: SMILES, ISO SMILES, InChI, InChI Key, formula, molecular weight, LogP, Rule of Five.
• Index those values into Spotlight and show them in Finder via Quick Look previews and thumbnails.
• Remain App Store compliant: sandbox-safe, predictable permissions, and no external converter dependencies.

Spotlight, Quick Look, and the macOS "superpowers"

This is the part that makes AtomLens feel "native" in a way most scientific tools do not: structures become searchable and previewable without opening the app. Spotlight indexing adds metadata to files (SMILES, InChI, InChI Key, formula, weight, LogP), and Quick Look turns Spacebar into an instant structure viewer.

We also built a Molecule Browser that queries Spotlight directly. It is essentially a local molecule database UI without the database - just the OS index.