ATOMLENS 3.1 / MAC HELPApp Store ↗

Browse Local Files

Local Molecule Files is the fastest way to search large local chemistry libraries without opening files one by one in Finder.

Browser layout

The Local Molecule Files browser starts with search, reaction-only, Finder-label, sort, and order controls. Results appear as cards in the central grid, and the bottom action bar holds label editing, sharing, Quick Look, Finder reveal, Managed Repository transfer, and Open Selected actions. Control-click a card to reach the same actions from its context menu.

On this page

Search and filter
Status messages
Result cards
Selection and preview
Spotlight and Finder labels

Search and filter

Type text into the filter field and press Return or click Search to search by filename and indexed chemistry metadata. AtomLens uses Spotlight chemistry keys when they are available and falls back to supported chemistry filenames when the richer metadata is missing or still catching up.

Show only Reactions limits the grid to indexed reaction files.
Finder-label buttons in the filter bar narrow the result set to matching label combinations.
Sort controls let you sort by modified date, creation date, molecular weight, or LogP in ascending or descending order.

Status messages

The bottom status bar reports the active browser operation. A spinner means AtomLens is still working; a blue progress bar appears when the current operation reports a determinate fraction, such as Managed Repository scanning, text-index rebuilding, background molecule-index validation, or repository deletion. The examples below use sample counts and search terms; the numbers and labels in your browser reflect the current search.

Local Files search

Example message	What it means
`Collecting molecule file references (1,240)...` `Collecting reaction file references for "Aspirin" (42)...`	AtomLens is collecting local-file references from Spotlight.
`Indexed chemistry metadata looks incomplete (12). Falling back to supported filenames...`	Spotlight returned too few chemistry metadata hits, so AtomLens starts a filename-based fallback search for supported chemistry formats.
`Collecting supported chemistry file references (320)...` `Collecting supported reaction file references for "Aspirin" (18)...`	AtomLens is collecting supported filenames because full Spotlight chemistry metadata is incomplete.
`Found 1,240 molecule files. Loading metadata...` `Found 320 supported chemistry files. Loading metadata...`	Reference collection is complete and AtomLens is about to load card metadata.
`Loading molecule metadata (350/1,240)...`	AtomLens is enriching result cards with chemistry metadata, dates, labels, and preview-ready values.
`Showing cached results. Refreshing metadata (350/1,240)...`	A warm-start cache is visible while AtomLens refreshes the same Local Files result set in the background.
`Loaded 1,240 molecule files.` `Loaded 42 reaction files.`	The active Local Files search finished.
`Local Files search could not start.` `Local Files search could not start filename fallback.`	The Spotlight query or fallback query could not be started.

Managed Repository search

Example message	What it means
`Scanning Managed Repository files...` `Scanning Managed Repository files (40,750/66,315, 61%)...`	AtomLens is reading repository references, applying repository filters, and preparing the result set. When counts are available, the progress bar uses the same fraction.
`Updating Managed Repository text index...` `Updating Managed Repository text index (40,750/66,315, 61%)...`	AtomLens updates the local text index in the background. Searches use the records already indexed, and results update as more records become available. Only changed records need to be indexed again.
`Search results may be incomplete while the text index updates.` `Text index update paused or incomplete. Search results may be incomplete.`	Some records are not yet searchable. Use the Pause or Resume icon beside the status text to control indexing. Committed results stay searchable, and resuming continues from saved progress. The text index is stored locally on each device, not in iCloud.
`Loading repository metadata (350/1,240)...`	The matching repository references are being converted into visible browser cards.
`Showing cached repository results. Refreshing metadata (350/1,240)...`	A cached default Managed Repository view is visible while AtomLens refreshes metadata for the current repository state.
`Loaded 1,240 Managed Repository files.` `Loaded 42 Managed Repository reaction files.` `Loaded 12 Managed Repository Markush structures.`	The active Managed Repository search finished.

Background repository activity

Example message	What it means
`Checking Managed Repository changes...`	The repository observer is checking content and metadata roots for changes, including iCloud-backed roots when sync is enabled.
`Validating molecule search index...`	AtomLens is checking or rebuilding the molecule search index used for repository chemistry search.
`Validating molecule search index (35%, scanning 23,000/66,315)...` `Validating molecule search index (72%, indexing 8,000/12,000)...`	The validation phase has item counts.
`Validating molecule search index (92%, writing cache)...` `Validating molecule search index (96%, updating cache)...`	The validation phase has a percentage but no item count.
`Uploading Managed Repository changes to iCloud...` `Downloading Managed Repository changes from iCloud...`	The macOS iCloud sync activity monitor reports repository upload or download activity.

Other status bar outcomes

Preparing to delete 12 Managed Repository entries..., Deleting Managed Repository entries..., and Deleting Managed Repository entries (8/12)... appear during repository-only deletion.
Showing 500 of 1,240 files (700 loaded). appears when the grid is showing a subset of the matching result set while loaded entries are still being tracked.
Empty-result messages can look like No indexed molecule or reaction files found., No molecule files found., No reaction files found., No Markush structures found., No Managed Repository files found., or No matching molecule files found..
Active-filter summaries can look like Active filters: Reactions only | Text: "Aspirin" | Labels: Red or Active filters: Markush structures only.
Idle can appear when the underlying search model has stopped and no search result state is active.

Result cards

Browser cards show more than thumbnails. A card can include structure preview, formula, path, created and modified dates, molecular weight, LogP, and Finder-label-aware styling.

The grid remains useful even when filenames are inconsistent because AtomLens surfaces chemistry metadata directly on the card.
Cards update as metadata and thumbnails arrive.
If AtomLens has not found supported chemistry files yet, it shows a clear empty-state message instead of an unexplained blank grid.

Selection and preview

The Local Molecule Files browser supports mouse and keyboard workflows.

Single-click for one file, Command-click for multi-select, Shift-click for ranges, and Command-A to select all visible results.
Double-click a card, press Return, or use Open Selected to open the current selection.
Press Space for in-app Quick Look without opening the file into a full document window.
Use Show in Finder when exactly one file is selected, or the Share button for standard macOS share destinations.
Use Managed Repository > Copy to Managed Repository to import copies of selected local files into AtomLens-managed storage.
Use Managed Repository > Move to Managed Repository... when you want AtomLens to import selected local files and then move the originals to the Trash. AtomLens asks for explicit confirmation before moving originals.
The Local Files panel never deletes arbitrary files. Deletion is available only for AtomLens-owned entries in the Managed Repository.

Spotlight and Finder labels

Local Molecule Files is deeply tied to macOS system metadata.

Spotlight makes chemistry identifiers and properties searchable outside AtomLens as well as inside the browser.
Finder labels are visible on cards, available as filters, and editable from the bottom toolbar.
Existing non-color Finder tags are preserved when you change labels from AtomLens.
Quick Look previews work in Finder and in the AtomLens browser flow.

Managed library workflow: If you want AtomLens-owned storage instead of broad local-file discovery, continue to Managed Repository and iCloud sync.

AtomLens 3.1 · Website guide updated 2026-10-18.