AtomLens Help Guide

Obscure Essentials

Updated: March 7, 2026

Contents

Quick Start

1. Open your chemistry file with File > Open... or Command+O. You can select one file or several files at once.
2. If you prefer to start with search, use File > Browse... or Option+Command+O to open Molecule Browser and find files by content.
3. If you already copied structure text, choose File > New, paste it, then click Parse & Render or press Command+Return.
4. Use the center canvas to inspect the drawing, then use the right sidebar to copy identifiers and review calculated properties.
5. If a source file contains many records, use File > Extract to split it into individual output files for easier downstream use.

Window Types

If a window is backed by a file, the title bar shows that file name and the macOS proxy icon. If you are working from pasted text only, the window title stays AtomLens until you save or export content.

User Interface Basics

Each document window is organized into three clear regions, so it is easy to understand where to type, where to inspect, and where to copy results:

• Left sidebar (Input): paste or type structure text, see format detection, clear input, and run parsing.
• Center panel (Canvas): interactive 2D drawing area for molecules or reactions.
• Right sidebar (Overview): copy-ready identifiers and computed values for the current molecule selection.

Toolbar actions and quick controls are designed to keep common tasks one click away:

• Open: open one or more files into new document windows.
• Browse: jump to Molecule Browser for Spotlight-based lookup across indexed files.
• Help: open this Help guide at any time without leaving your current workflow.
• Hide or Show Input Sidebar: Command+0.
• Hide or Show Overview Sidebar: Option+Command+0.

You can resize both sidebars by dragging the vertical divider lines, so you can prioritize the canvas or the text and details area as needed.

Canvas Interaction and Style Controls

The center canvas is where you inspect structures visually. Molecules and reactions use the same interaction model, so once you learn these controls, the experience stays consistent.

• Pan: click and drag in the canvas area to move around comfortably.
• Zoom: use the zoom slider, mouse wheel, or trackpad pinch to focus on fine details.
• Rotate: use the rotation slider or trackpad rotation gesture to change orientation.
• Reset: return to the default view at any time if you want to start fresh.
• Snapshot: copy a transparent PNG of the current drawing directly to the clipboard for reports or slides.

Style toggles in the toolbar help you adapt the drawing to your current task and audience:

• Show Carbons: show or hide explicit carbon labels.
• Element Colors: color-code atoms by element type.
• Color Bonds: color bonds to match atom color mode when available.
• Aromatic Circles: switch aromatic ring visualization style.
• Map Colors: in reaction mode, highlight mapped atoms when map indices exist.
• Map Numbers: in reaction mode, show atom-map numbers when present.

Overview Sidebar

The Overview sidebar is your quick reference panel for the currently selected molecule context. It is especially useful when you need copy-ready identifiers, fast property checks, or quick confirmation before exporting.

• If a file has multiple molecules, use the picker at the top to move between entries.
• Common values include formula, mass values, heavy atom count, H-bond counts, ring count, and Rule of Five status.
• SMILES, ISO SMILES, InChI, and InChI Key include one-click copy buttons for fast reuse.
• In reaction mode, click a specific participant first to inspect that participant's details in the sidebar.

Molecule Browser

Molecule Browser is the fastest way to navigate large local chemistry libraries. Instead of opening files one-by-one in Finder, you can search, sort, preview, and open results from one window. This is especially helpful when file names are inconsistent but metadata and structures are known.

• Search: type a keyword and press Return or click Search to run a query.
• Sort: sort by Modified Date, Creation Date, Molecular Weight, or LogP in ascending or descending order.
• Selection: single-click for one file, Command-click for multi-select, Shift-click for ranges.
• Open: double-click a card, press Return, or click Open Selected.
• Quick Look: press Space to preview content without opening the file in a document window.
• Reveal in Finder: use Show in Finder when exactly one file is selected.

Extract Tools

Extract tools are built for one-file-in, many-files-out workflows. AtomLens first validates the source file, then asks where to save results, and then writes each output file with clear progress feedback. This is useful for cleanup, QA, and handoff workflows where each record should live in its own file.

Split multi-structure SDF into multiple files

1. Choose File > Extract > Split multi-structure SDF into multiple files....
2. Select an SDF file that contains two or more structures.
3. Confirm the detected structure count and choose a destination folder.
4. AtomLens writes one .sdf file per structure and shows progress while saving.

Split multi-reaction SMILES into multiple files

1. Choose File > Extract > Split multi-reaction SMILES into multiple files....
2. Select a multi-line Reaction SMILES source file.
3. Confirm the number of valid reactions and choose a destination folder.
4. AtomLens writes one .rsmi file per valid reaction.

Split multi-reaction SMILES into multiple RXN files

1. Choose File > Extract > Split multi-reaction SMILES into multiple RXN files....
2. Select a multi-line Reaction SMILES source file.
3. Confirm the count, choose a destination folder, and start extraction.
4. AtomLens converts each valid reaction entry into an individual .rxn file.

If invalid Reaction SMILES lines are present, AtomLens skips them and includes the skipped count in the final status message. This helps you complete large extraction jobs while still seeing exactly what needs review.

Chemical Reaction Support

AtomLens supports reaction files directly, including .rsmi, .rxn, and .rdf. You can open them from Finder, from File > Open..., or from Open Recent, just like molecule files.

• Reaction drawings include reactants, agents, products, plus signs, and reaction-arrow layout.
• The same pan, zoom, rotate, reset, and snapshot tools work in reaction mode.
• Reaction documents use a split layout: drawing on top, participant table below.
• The participant table is grouped by role with quick preview values for reactants, agents, and products.
• Selecting a participant updates the Overview sidebar so you can inspect that piece in detail.
• If atom-map numbers are available, Map Colors and Map Numbers are enabled automatically.

Reaction files are also supported in Quick Look previews and indexed into Spotlight metadata for local searching. This means you can discover and preview reaction content quickly even before opening full documents.

Supported Input Formats

AtomLens can open common molecule and reaction file types directly. If you are not sure what a format means, you can still open it and review the content visually before deciding what to do next.

Supported Export Formats

Use File > Export... to export the currently selected molecule context. In day-to-day workflows, SVG, SDF, and SMILES are usually the most common choices for sharing and downstream tooling.

Spotlight and Quick Look

AtomLens integrates with Finder so you can work faster without manually opening every file:

• Spotlight: AtomLens stores searchable chemistry metadata for local file lookup.
• Quick Look: you get visual previews in Finder, including reaction files, before opening.
• Molecule Browser: uses those indexed fields to keep search and card browsing responsive.

Spotlight Metadata Fields

This section is mainly for advanced users and scripting workflows. AtomLens writes metadata keys prefixed with de_losko_atomlens_ so you can build precise local searches.

Spotlight Search Examples

These Terminal examples are optional. You only need them if you want command-line filtering outside the app.

Find by exact InChI Key

mdfind 'de_losko_atomlens_inchi_key == "HVQAJTFOCKOKIN-UHFFFAOYSA-N"'

Find all AtomLens-indexed chemistry files

mdfind 'de_losko_atomlens_is_molecule == 1'

Find only reaction files

mdfind 'de_losko_atomlens_is_reaction == 1'

Find by molecular-weight range

mdfind 'de_losko_atomlens_molecular_weight >= 200 && de_losko_atomlens_molecular_weight <= 300'

Find Rule-of-Five compliant compounds

mdfind 'de_losko_atomlens_rule_of_five_compliant == 1'

Settings and Permissions

AtomLens keeps settings minimal on purpose. Most users only need to decide whether Molecule Browser should open automatically at launch. This keeps setup simple while still covering the most common preference.

• Open the Molecule Browser when launching AtomLens: enabled by default and useful if you usually start from search instead of opening a known file.
• Grant Access... (Home folder): optional permission helper for smoother reopen and search behavior in sandboxed macOS environments.

Troubleshooting

If something does not behave as expected, the checks below usually resolve it quickly. They cover the most common causes reported in everyday use.

• Parse button is disabled: your input is empty, or AtomLens cannot detect a supported structure format yet.
• Extract workflow stops early: the selected source likely has only one valid record, and Extract requires multiple records.
• Map controls are disabled in reaction mode: the current reaction does not include atom-map numbers.
• A file does not reopen from Search or Open Recent: open it once through the file picker and grant access if macOS asks.

Third-Party Software and Licenses

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

Privacy Notice

AtomLens is built for local-first desktop use. The points below summarize what that means in practice.

• AtomLens processes chemistry content locally on your Mac.
• No account or login is required for normal use.
• No cloud upload is required for parsing, viewing, browsing, exporting, or extraction workflows.
• Spotlight and Quick Look maintain local macOS indexes and preview caches.
• Export and extraction files are written only to destinations you explicitly choose.

Questions or bug reports: support@losko.de.

© 2026 Sascha Losko — Obscure Essentials. All rights reserved.