AtomLens Help Guide

Obscure Essentials

Updated: February 23, 2026

Contents

Quick Start

1. Open a molecule with File > Open…, File > Open Recent, or by double-clicking a supported file in Finder.
2. AtomLens opens each selected file in its own window and renders it automatically.
3. Use File > New to create an empty window for pasted or typed structure text.
4. When entering text manually, click Parse & Render to display the structure.
5. Review identifiers and calculated properties in the right sidebar.

Main Workflow

A typical AtomLens session starts by opening one or more molecule files. The structure is shown immediately in the center canvas, while key descriptors such as SMILES, InChI, InChI Key, formula, and molecular properties are summarized in the overview panel. You can then refine visual style, inspect stereochemistry, rotate the view, and export results in the format required for your next step (reporting, sharing, or downstream analysis).

Interactive Molecule Graphics (Metal Canvas)

AtomLens draws molecules on a native Metal canvas for smooth, high-quality interaction. You can explore the same structure from different visual angles and scales without leaving the main window.

To zoom, you can use the zoom slider in the canvas controls, a mouse wheel, or a trackpad pinch gesture. To pan, drag the canvas with the mouse or trackpad. To rotate, use the rotation slider (0-360 degrees) or the trackpad rotation gesture. Labels stay attached to their atoms while the structure rotates, and labels remain upright for readability. The Reset button returns to the default view.

AtomLens also offers quick style switches that help in different scientific contexts. Show Carbons displays explicit carbon labels at vertices; when it is off, AtomLens follows the standard skeletal-formula convention where carbon is implied. Element Colors colors atom labels by element type, which helps separate heteroatoms from carbon-rich scaffolds at a glance. Color Bonds extends color coding to bonds to make local connectivity and functional-group boundaries easier to follow in dense structures. Aromatic Circles displays aromatic rings with circle annotations that indicate delocalized pi-electron systems (the common aromatic representation used in chemical communication, complementing alternating-bond drawings).

The Snapshot button copies a transparent PNG of the current view (including style, zoom, and rotation) to the clipboard. You can paste that image directly into applications such as Microsoft PowerPoint or Microsoft Word.

Molecule Browser

The Molecule Browser is a dedicated window for navigating large local molecule collections. Open it from File > Browse… or the toolbar Browse button. It stays open while you continue working, so you can open compounds into new AtomLens windows without losing your place.

For very large libraries, AtomLens first collects matching molecule files, then enriches each card with chemistry metadata, and finally loads image previews only for what is on screen (plus a small buffer for smooth scrolling). This keeps browsing responsive even with large corpora.

Search is intentionally explicit: enter a keyword and press Return (or click Search) to run a new search. This avoids constant re-querying while you type and keeps the browser responsive on large datasets. You can search by filename and indexed chemistry keywords, which is useful when you remember only part of a compound name, identifier, or annotation.

Sorting lets you reorganize the same result set by what matters for your task. You can sort by modification date, creation date, molecular weight, or LogP, and choose ascending or descending order. In practice, this makes it easy to surface the newest structures, historical records, or compounds in a target physicochemical range.

You can select one or many cards and open them together. Double-click opens immediately. Keyboard navigation is supported with arrow keys, Return opens the current selection, and Space toggles Quick Look preview. If exactly one card is selected, Show in Finder reveals that molecule file in its enclosing Finder folder with the file preselected. The browser remembers its window size between launches.

Window Behavior

• New: opens an empty AtomLens window.
• Open / Open Recent / Finder double-click: opens the selected molecule in a new window.
• Close: closes only the active window.
• Window title: file-backed windows show file name + proxy icon; non-file windows keep the title AtomLens.

Settings

• Open Molecule Browser upon launch (default: enabled): opens the browser automatically when AtomLens starts.
• Grant access to home folder: requests Home-folder permission for smoother sandboxed file access.

Supported Input Formats

Supported Export Formats

Use File > Export… and choose a format in the save dialog.

Extract: Split Multi-Structure SDF

1. Choose File > Extract > Split multi-structure SDF into multiple files….
2. Select an SDF file that contains more than one structure.
3. AtomLens reports the number of structures and asks for a target folder.
4. Each structure is saved as an individual .sdf file (using molecule name where available).
5. A progress dialog shows real-time save progress and any failed entries.

Why Spotlight and Quick Look Matter

In real lab workflows, filenames alone are rarely enough. AtomLens writes chemistry-aware metadata into Spotlight and provides visual previews through Quick Look. This means you can find likely candidates quickly, inspect them before opening, and reduce context switching during analysis.

Spotlight Metadata Attributes

AtomLens writes dedicated metadata keys prefixed with de_losko_atomlens_.

Spotlight Search Examples (Advanced)

Examples for Terminal-based search:

Find by exact InChI Key

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

Find all molecule files indexed by AtomLens

mdfind 'de_losko_atomlens_is_molecule == 1'

Find molecule files by keyword (name or indexed keywords)

mdfind 'de_losko_atomlens_is_molecule == 1 && (kMDItemDisplayName == "*flavonol*"cd || kMDItemKeywords == "*flavonol*"cd)'

Find by molecular-weight range

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

Find by LogP threshold

mdfind 'de_losko_atomlens_xlogp > 3.0'

Find Rule-of-Five compliant compounds

mdfind 'de_losko_atomlens_rule_of_five_compliant == 1'

Chemistry Notes

• Depictions are optimized for communication and review workflows (2D schematic representation).
• AtomLens follows CDK-derived depiction conventions for rings, aromaticity, and stereobond presentation.
• 2D drawings are not a substitute for full 3D conformational analysis.

Third-Party Software and Licenses

InChI and InChI Key generation in AtomLens uses the native Swift chemistry stack. No external InChI runtime library is required for normal use.

CDK Source and Scientific References

The Swift package used by AtomLens: https://github.com/SaschaLosko/CDKSwiftNativePort

CDKSwiftNativePort was created to support AtomLens and is based on the original Chemistry Development Kit (CDK). Please cite the original CDK literature in scientific work where appropriate:

1. Willighagen et al. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J. Cheminform. 2017; 9(3), doi:10.1186/s13321-017-0220-4
2. May and Steinbeck. Efficient ring perception for the Chemistry Development Kit. J. Cheminform. 2014, doi:10.1186/1758-2946-6-3
3. Steinbeck et al. Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. Curr. Pharm. Des. 2006; 12(17):2111-2120, doi:10.2174/138161206777585274
4. Steinbeck et al. The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. J. Chem. Inf. Comput. Sci. 2003 Mar-Apr; 43(2):493-500, doi:10.1021/ci025584y

Privacy Notice

• AtomLens processes your molecule content locally on your Mac.
• AtomLens does not upload structures to a cloud service as part of normal workflows.
• Spotlight and Quick Look keep local macOS indexes/caches for search and preview.
• Recent files are managed by macOS for the Open Recent workflow.
• Exports are written only to locations you explicitly choose.

Feedback and support

For feedback, bug reports, or feature requests, email support@losko.de.

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