Managed Repository and iCloud Sync

Repository panel

Managed Repository is the managed-library browser for AtomLens-owned chemistry files. It intentionally matches Local Molecule Files so the same grid browsing, sort controls, Quick Look, sharing, and Finder reveal flow work there as well.

• Use Local Molecule Files for broad Spotlight-backed discovery across chemistry files already on your Mac.
• Use Managed Repository for AtomLens-managed entries you want to keep as a library.
• On macOS, Search Managed Repository is available as an AtomLens action in the Shortcuts editor. It opens this window and runs the requested text in the existing repository search; Spotlight file indexing remains handled separately by the metadata importer. For variable Siri searches, create a personal shortcut that asks for text, passes the provided input to the AtomLens action's Text field, and has a memorable name such as Search in AtomLens. Invoke that personal shortcut by its name; Siri then asks for the search term.
• Managed Repository cards focus on library metadata and previews. They do not show the filesystem path for the managed copy.
• The browser refreshes from shared repository observation, so content and metadata changes can flow back into the browser automatically.
• For scan, cache, text-index, molecule-index, and sync messages shown in the bottom status bar, see browser status messages.
• On macOS, card context menus mirror the bottom action bar. Repository entries can be deleted from the bottom Delete... button, from a card context menu, or with Backspace after selection.
• Command-A selects all visible Managed Repository results on macOS, so multi-entry deletion and sharing can use the same selection model as Local Files.
• On iPad, each repository card has compact icon buttons for tags, sharing, and deletion. Tapping the card itself opens the item.

Automate chemistry documents with Shortcuts

In Apple's Shortcuts app, add an action and search for AtomLens. On Mac and iPad with OS 26 or later, use Find Chemistry Documents, Open Chemistry Document, Get Chemistry Document Properties and Export Chemistry Document. These actions work with documents saved in the Managed Repository. The existing Mac Search Managed Repository action continues to open the browser.

1. Add Find Chemistry Documents. Enter a name or keyword; optionally choose molecule/reaction type, a color label or molecular-weight bounds. The default result limit is 20, with a maximum of 500.
2. For a single document, pass one result to Get Chemistry Document Properties to calculate its properties, or to Open Chemistry Document to view it in AtomLens.
3. Pass that document to Export Chemistry Document and choose Original, SVG, PNG, PDF or a compatible chemical format. Add Apple's Save File or Quick Look action to use the returned file.

On macOS/iPadOS 27, Export Chemistry Documents and Get Properties of Chemistry Documents process a selection in one action. For example, find documents with a color label, pass the results to Export Chemistry Documents using Original, then pass the returned files to Save File. Batches support up to 500 selected identifiers and 32 MiB of combined output. Duplicate selections are processed once; exports with the same filename receive numbered suffixes.

Find, property calculation and export show progress during long operations on OS 27. Cancel through the initiating system interface when a Stop control is offered. Cancellation takes effect between processing stages; a chemistry calculation already underway may need to finish first. A cancelled or failed batch does not return a partial selection of files.

Property calculation and format conversion support single-structure documents up to 8 MiB. Use Original to preserve a complete multi-structure or multi-reaction file. For an Original larger than the batch output limit, use the single-document export action. Incompatible molecule/reaction formats produce an explanatory error.

Document references follow the saved item when its name changes. A document must be available on the device running the shortcut; iCloud delivery may still be pending. On OS 27, saved documents and visible library cards also provide document context to Apple's system index. Unsaved edits and unrelated external files are excluded from that saved-document context.

You can invoke a personal shortcut by its name through Siri, using the language configured for Siri. AtomLens supplies English and German action names. These actions process chemistry on-device and add no PubChem request or document upload.

Import from PubChem

Choose PubChem in the Managed Repository toolbar. Enter a name, synonym, compound ID (CID), substance ID (SID), formula, SMILES, InChI, or InChIKey and choose Search. Automatic detects common input formats; choose a specific Search as type for ambiguous input. Other identifiers include registry and database identifiers such as CAS numbers.

Results appear as structure cards in a separate, movable and resizable window on Mac, or a dialog on iPad. Use Load More Results for another page, then choose Import on an individual card. The original 2D SDF and its PubChem properties are saved as PubChem-CID.sdf in the current repository, with the PubChem molecule name as its display name, and the library refreshes. Matching query text is highlighted in visible names, CIDs, and formulas. PubChem may also match synonyms that are not shown on the card. There is no multiple selection or bulk download. An added card stays marked for the current search session.

Searches send your input to PubChem PUG REST over the internet. Previews are drawn locally. AtomLens serializes searches and downloads below five requests per second and backs off when PubChem is busy. You can cancel a pending request; a repository write that has already begun finishes safely. Imported files use the same local or iCloud repository location as other managed files.

Example structures and reactions

The Managed Repository can be seeded with bundled example data for a first-run tour, demos, training, and App Store review. The importer adds 20 ChEBI Entity of the Month structures and 20 Rhea-derived reactions.

• The Welcome screen offers Add example structures and reactions. The option is checked by default only when the repository starts empty.
• The same importer is available later in Settings > Managed Repository with Add Example Structures and Reactions.
• Examples are stored in the same Managed Repository location as user-saved entries, using iCloud when repository sync is enabled and available.
• Duplicate checking compares molecule InChIKeys and reaction long RInChIKeys, so rerunning the importer skips examples already present in the repository.
• After import, open File > Managed Repository... and use search, Quick Look, the reactions-only filter, or direct card opening to inspect the examples.

Saving files to the repository

Use File > Save to Managed Repository... when you want AtomLens to create a managed copy of the current chemistry context.

• The repository-save flow accepts only chemistry formats that AtomLens can reopen directly in a molecule window or a reaction window.
• Visual outputs such as SVG stay in Export and Share flows. They are not offered as repository-save formats.
• On macOS, repository entries can be added through Save to Managed Repository... or from selected Local Files cards with Copy to Managed Repository.
• Move to Managed Repository... imports the selected Local Files entries and, after confirmation, moves the originals to the Trash.
• Synced content from other devices can also appear here automatically.

Sync behavior

Use the same Apple Account on Mac and iPad and enable Sync chemical files over iCloud under Settings > Managed Repository on each device. AtomLens syncs managed chemistry content, tags, favorites, and recent use through your private iCloud storage when available.

• Received changes refresh the repository automatically. The first sync of a large library can take time; keep AtomLens open and check repository status while it progresses.
• iCloud temporarily paused — retrying automatically means Apple's service is busy or temporarily limiting requests. AtomLens keeps saved content, and Apple schedules the retry. The details may show the time after which Apple requested a retry; this is not a completion estimate. Account, storage and conflict warnings remain separate.
• Search indexes, thumbnails, Files, and system search can catch up after content arrives. An upload/download indicator is progress information, not a guarantee that every other device has received all changes.
• Files merely opened from arbitrary folders and depictions handed to Share are not automatically added to repository sync. Save a managed copy when it belongs in the shared library.

Synced metadata and Finder labels

While AtomLens runs on macOS, managed repository tags can be mirrored to Finder labels for materialized files. iPad exposes managed files and tags through Files.

• Repository tags, favorites, and recent use are included in sync.
• Finder label changes made in the repository browser remain visible both in AtomLens and in Finder.
• Remote synced tag changes can be reflected back into Finder while AtomLens is active, which keeps cross-device label state more coherent.

When sync is off

If you turn off Sync chemical files over iCloud in macOS AtomLens Settings, the Managed Repository remains available and stores content locally on this Mac.

• Local Files continues to provide broad Spotlight-backed discovery across files outside AtomLens.
• The Managed Repository panel, toolbar button, File menu item, and save workflow stay visible.
• On iPad, Managed Repository, Save, extraction results, Files, Quick Look, and repository search continue to use the local Managed Repository.
• You can turn sync back on later from Settings to move managed content back to iCloud when available.

© 2026 Dr. Sascha Losko - Obscure Essentials. All rights reserved.