AtomLens 3.1 Help

AtomLens turns supported chemistry text and files into interactive 2D and 3D molecule views and 2D reaction views, calculated identifiers, properties, and shareable exports. It works with common molecule and reaction formats, supports direct text input such as SMILES, InChI, Reaction SMILES, and RInChI, and can convert supported IUPAC names into rendered structures.

Beyond a single document window, AtomLens integrates with macOS so chemistry files remain useful in Finder, Quick Look, Spotlight, Local Molecule Files, and Managed Repository. Use the Managed Repository when you want AtomLens-owned chemistry files that remain available locally and can sync through iCloud when repository sync is enabled.

1. If you do not have chemistry files at hand, use the Welcome screen or Settings > Managed Repository > Add Example Structures and Reactions to import the bundled examples.
2. Open a chemistry file, or choose Edit Structure Source in the document toolbar, paste supported text and choose Apply & Render.
3. Use Browse Local Files when you want Spotlight-backed discovery across chemistry files already on your Mac.
4. Use Save to Managed Repository... when you want AtomLens to keep a managed copy in the Managed Repository.
5. Open Settings if you want to change launch behavior, repository sync, or sandbox access.

AtomLens includes example structures and reactions so you can try the app immediately without downloading or locating chemistry files first. The set contains 20 ChEBI Entity of the Month structures and 20 Rhea-derived reaction examples, including reaction entries stored through RInChI for repository import.

1. On first launch, leave Add example structures and reactions selected on the Welcome screen, then choose Continue.
2. If the Welcome screen is no longer shown, open Settings > Managed Repository and choose Add Example Structures and Reactions.
3. Open File > Managed Repository... to browse the imported examples, then use the repository search field or the reactions-only filter to narrow the grid.
4. Open a structure or reaction card to inspect the depiction, calculated properties, identifiers, and reaction participants.

AtomLens compares structure InChIKeys and reaction long RInChIKeys during import, so importing the examples again skips entries that are already present instead of adding duplicates.

AtomLens is a local-first macOS app. Parsing, viewing, exporting, and extraction happen on your Mac. When repository sync is enabled, managed repository content and managed repository metadata move through iCloud when available. Finder labels, Spotlight metadata, and Quick Look previews are integrated so that AtomLens stays useful even outside the main document window.