Settings panes

AtomLens keeps settings grouped into focused panes:

• Workspace: includes Open the Molecule Browser when launching AtomLens .
• Managed Repository: includes Sync chemical files over iCloud . Turning it off keeps the Managed Repository available and stores its content locally on that Mac or iPad.
• Text Size: controls one Help-browser scale plus practical UI text-size choices used across AtomLens surfaces.
• Permissions: includes the helper for granting smoother sandbox access to the home folder.
• Experimental Features: keeps optional features separate from stable release behavior.
• MCP Server: configures local stdio and HTTP access for automation clients.
• Shortcuts and About provide reference information without leaving the app.

Permissions

In sandboxed macOS environments, AtomLens may need file access grants for smoother reopen, search, Quick Look, and Finder-label update behavior.

• If a file does not reopen from Search or Open Recent, open it once through the file picker and grant access if macOS asks.
• If Finder labels do not update from Molecule Browser, grant access to the relevant location and try the label action again.
• The optional Grant Access... helper exists to reduce repeated friction for frequently used locations.

Finder and Spotlight

AtomLens integrates with macOS system surfaces so that chemistry files remain useful outside the main app window.

• Quick Look: chemistry previews are available in Finder and inside Molecule Browser.
• Spotlight: AtomLens writes searchable chemistry metadata for local file lookup.
• Finder labels: Molecule Browser reads native label and tag metadata, filters by it, and can write selected label changes back to files.

Common metadata key	Meaning
de_losko_atomlens_is_molecule	General chemistry index flag used by Molecule Browser queries.
de_losko_atomlens_is_reaction	Reaction-specific index flag.
de_losko_atomlens_smiles	Representative or generated SMILES.
de_losko_atomlens_inchi_key	Generated InChI Key.
de_losko_atomlens_formula	Molecular formula.
de_losko_atomlens_molecular_weight	Molecular weight in daltons.
de_losko_atomlens_xlogp	XLogP estimate.
de_losko_atomlens_rule_of_five_compliant	Rule-of-Five compliance flag.

Useful Terminal examples

mdfind 'de_losko_atomlens_is_molecule == 1'
mdfind 'de_losko_atomlens_is_reaction == 1'
mdfind 'de_losko_atomlens_inchi_key == "HVQAJTFOCKOKIN-UHFFFAOYSA-N"'

MCP service

AtomLens includes a bundled MCP helper and a local MCP Server settings pane for external clients such as Codex. In a standard macOS installation, the helper lives at /Applications/AtomLens.app/Contents/Helpers/atomlens-mcp .

• For stdio MCP clients, launch atomlens-mcp directly.
• For HTTP JSON-RPC clients, open Settings, select MCP Server , choose the port, keep or create the required bearer token, then start the server.
• Use Create to generate a bearer token, and enable Launch at login when the HTTP server should stay available after signing in even if AtomLens is not open.
• The local HTTP endpoint binds to 127.0.0.1 only and defaults to http://127.0.0.1:8080/mcp .
• HTTP requests must include the configured bearer token. The helper rejects request bodies larger than 1 MiB before reading them.
• The launch-at-login helper reads the app-written MCP configuration from Application Support and exits without listening if that configuration is missing a bearer token.
• The Codex connector toggle edits ~/.codex/config.toml . AtomLens may ask for Home folder access before installing it.
• The current MCP surface covers repository search, add, batch get, exact identifier lookup, export, delete, color labels, favorites, and recent-use metadata.

Codex configuration

[mcp_servers.atomlens]
command = "/Applications/AtomLens.app/Contents/Helpers/atomlens-mcp"
enabled = true

After saving the Codex config, restart Codex so it reloads the MCP server list.

Troubleshooting

• Parse button is disabled: the current input is empty or AtomLens cannot detect a supported structure format yet.
• Molecule Browser shows no files: Spotlight may still be indexing, or AtomLens has not found supported chemistry filenames yet.
• Finder-label filters hide everything: active Finder-label filters are combined, so a result must match every selected label.
• Extract stops early: the source probably contains only one valid record, while Extract requires multiple records.
• Map controls are disabled in reaction mode: the current reaction does not include atom-map numbers.
• Need reaction artwork: use File > Share > Share as SVG , PNG, or PDF for visual whole-reaction output. Use RXN, RDF, Reaction SMILES, RInChI, or CML when you need chemistry file export.

Privacy and licenses

AtomLens is local-first desktop software.

• Parsing, viewing, browsing, exporting, and extraction happen locally on your Mac.
• No account or login is required for normal use.
• Spotlight and Quick Look maintain local macOS indexes and preview caches.
• Export and extraction output is written only to destinations you choose explicitly.

Component	Role in AtomLens	License
CDKSwiftNativePort	Parsing, depiction, identifier generation, reaction support, and chemistry property calculation.	LGPL-2.1-or-later
OPSINSwift	On-device translation of supported IUPAC names into renderable chemistry input.	Apache-2.0

CDKSwiftNativePort repository: https://github.com/SaschaLosko/CDKSwiftNativePort

OPSINSwift repository: https://github.com/SaschaLosko/OPSINSwift