Browse and Files

Use Managed Repository, Files integration, and tags to find saved chemistry quickly.

What Managed Repository searches

Managed Repository is the primary iPad workspace for AtomLens-owned chemistry. Its Search button runs indexed full-text search across saved names, formulas, identifiers, chemistry text, tags, and source filenames. It does not perform desktop-style Spotlight search across the whole device.

• Press Return or tap Search to rank indexed matches by relevance; clearing the search restores your previous sort.
• Use Reactions only, Markush only, 3D only, and tag filters to narrow the repository.
• Sort by relevance, added, modified, or creation date, name, type, molecular weight, or LogP.
• Tap Search by Query Structure to open the full Ketcher drawing editor, draw or edit a visual query, and choose Substructure or Similarity. You can also seed the editor from the current molecule or imported MOL, SDF, SMILES, or CXSMILES text.
• Each molecule card's structure-search menu can find similar structures at a chosen Tanimoto threshold or use that molecule as a substructure query.

Import from PubChem

Tap PubChem in the Library toolbar. Enter a name, synonym, compound ID (CID), substance ID (SID), formula, SMILES, InChI, or InChIKey, then tap Search. Automatic detects common input formats; use Search as when an input is ambiguous.

Review the structure cards and tap Import on the compound you want. AtomLens uses the PubChem name as its Library display name and preserves the original SDF and its properties. Load More Results retrieves another page. Imports are individual; there is no multiple selection or bulk import. Matching query text is highlighted in visible names, CIDs, and formulas; matches in other PubChem synonyms may not be visible.

Searching sends your query to PubChem over the internet. Previews are drawn locally. Searches and downloads share a paced request queue and pause when PubChem is busy. Cancel stops a pending request; a repository write that has already begun finishes safely.

Files app integration

AtomLens exposes its internal library through Files using a File Provider domain. That gives saved structures and extraction results a stable place in the iPad workflow.

Enable Sync chemical files over iCloud in Settings > Managed Repository on each device, using the same Apple Account. AtomLens syncs managed chemistry content, tags, favorites, and recent use through your private iCloud storage.

If you turn iCloud sync off in Settings, this iPad keeps repository-backed Save, Extract, Browse, Files, Quick Look, and search features available through the local Managed Repository.

• Files tags applied to AtomLens-owned files show up inside Managed Repository.
• Files can reopen AtomLens-owned files directly back into the app.

Previews, sharing, and expectations

AtomLens supports system Quick Look previews for supported chemistry files on iPad. Managed Repository cards show depiction thumbnails and chemistry metadata inside AtomLens for fast scanning and sharing.

• Use Share from a repository card when you want to send a saved file to another app.
• From Files, you can Quick Look AtomLens-owned files without reopening them in the app.
• System search coverage is narrower on iPad than on Mac. AtomLens donates Managed Repository items to Core Spotlight, but not every arbitrary chemistry file on the device.
• Changes received from iCloud refresh the Managed Repository and its system integrations. Initial sync of a large library can take time; check repository status while it progresses.
• Cross-device timing still depends on iCloud delivery and when AtomLens or Files wakes again.