AtomLens Help
AtomLens is a local-first chemistry workspace for opening, rendering, inspecting, exporting, and organizing molecule and reaction files on Mac and iPad.
AtomLens turns supported chemistry text and files into interactive 2D structure 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 the system so chemistry files remain useful in Finder, Files, Quick Look, Spotlight, and the Molecule Browser where each platform supports them. 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.
Quick Start
- 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.
- Open a chemistry file or paste supported structure text into a document window.
- Use Browse Local Files when you want Spotlight-backed discovery across chemistry files already on your Mac.
- Use Save to Managed Repository... when you want AtomLens to keep a managed copy in the Managed Repository.
- Open Settings if you want to change launch behavior, repository sync, or sandbox access.
Quick Start With Examples
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.
- On first launch, leave Add example structures and reactions selected on the Welcome screen, then choose Continue .
- If the Welcome screen is no longer shown, open Settings > Managed Repository and choose Add Example Structures and Reactions .
- Open File > Managed Repository... to browse the imported examples, then use the repository search field or the reactions-only filter to narrow the grid.
- 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.
Task Guides
Understand the main document window, render pasted structures, inspect metadata, and export or share molecule results.
Search local chemistry files, filter and sort results, preview with Quick Look, and work with Finder labels.
Learn how the managed repository works on Mac and iPad, how iCloud sync behaves, and what happens when sync is turned off.
Review the Settings panes, sandbox access, Spotlight and Finder integration, AtomLens MCP setup, and common troubleshooting steps.
Reference Guides
See supported input and export formats, extraction workflows, reaction features, CXSMILES and Markush notes, and roundtrip expectations.
Look up the chemistry terms, identifiers, calculated properties, reaction concepts, and file formats used throughout AtomLens.
Support Notes
AtomLens is local-first. Parsing, viewing, exporting, and extraction happen on your device. When repository sync is enabled, managed repository content and managed repository metadata move through iCloud when available. Finder labels, Files tags, Spotlight metadata, and Quick Look previews are integrated where the platform supports them so AtomLens stays useful even outside the main document window.