Work With Structure Documents

Opening documents

You can open chemistry files from Finder, from File > Open..., from Open Recent, from Local Molecule Files, or from the Managed Repository browser. AtomLens opens common molecule formats, reaction formats, plain-text chemistry inputs, and modern notation such as CXSMILES when it is embedded in supported text input.

• Use a document window when you already know which file or text you want to inspect.
• Use Browse Local Files... on macOS when you want to discover arbitrary local files first. On iPad, Library returns to the same search and filters; Open Documents resumes your tabs.
• Reaction documents can be inspected as complete reactions, exported as reaction files, or saved participant-by-participant when you need individual structures.

Input and render

Choose Edit Structure Source or Edit Reaction Source in the toolbar. The large editor accepts supported chemistry text and stages changes until Apply & Render. Cancel leaves the document unchanged.

• Enter an IUPAC name… converts a supported name into structure source in the editor. Apply the result to update the document.
• Use the source editor to review or replace SMILES, InChI, MOL/SDF, or reaction text.
• Draw Structure or Draw Reaction opens a separate drawing editor. Apply its changes to update the current document.
• For a new drawing, File > New opens the Chemical Drawing Editor. See the drawing workflow.

Search with the current molecule (macOS)

Use Search in a molecule window's toolbar to search the Managed Repository with the displayed structure.

• Find Similar Structures… asks for a minimum Tanimoto similarity score between 0 and 1, then opens ranked results.
• Find Substructure Matches finds repository molecules that contain the displayed structure.
• For a file containing several molecules, the query is only the currently displayed molecule. Applied edits are included; saving or importing the query into the repository is not required.
• Results open in a separate window. The source document and any existing browser search remain available. Search is disabled for an empty document or a reaction.

Canvas and style tools

The center canvas is interactive. You can zoom, rotate, reset, and take a snapshot without leaving the document window.

• The zoom and rotation sliders change the active depiction immediately.
• Snapshot captures the current view as an image of the drawing area.
• Use the pin beside Reset to keep the molecule or reaction HUD visible. The filled pin means Pinned; the crossed-out pin means Unpinned. Each new canvas starts unpinned, and unpinning restores the usual fading after inactivity.
• The toolbar exposes depiction-style controls such as element colors, bond colors, aromatic circles, highlight style, and related drawing options.
• Reaction documents use the same interaction model for the drawing section, with additional reaction-aware controls when atom-map information is available.

2D and 3D molecule views

The molecule canvas offers a 2D/3D selector. Whole reactions remain in 2D. A 3D view is a visualization, not proof of an experimentally measured or energy-minimized conformation.

• Ball shows balls and sticks, Stick emphasizes bonds, and CPK uses space-filling spheres.
• Use the palette control for atom colors. CPK representation and the CPK color palette are separate choices. See available palettes and attribution.
• Drag with the mouse or click-drag on the trackpad to turn the 3D model. Scroll with two fingers to move it across the canvas, pinch to zoom, and twist two fingers to roll. A mouse wheel also zooms. Trackpad scrolling follows your macOS scrolling preference; in 2D, dragging moves the drawing.
• Snapshot captures the current 3D view as PNG. File > Share and SVG export use the 2D depiction, including PNG/PDF share formats.
• On iPad, drag with one finger to turn the 3D model and with two fingers to move it across the canvas. Pinch to zoom and twist two fingers to roll. Auto-Rotation pauses during gestures and resumes when they finish on both platforms. Turn it off for a still orientation. The X, Y, and Z sliders, Reset, and Snapshot remain in the HUD.

Overview sidebar

The Overview sidebar summarizes what AtomLens knows about the current structure or selected reaction participant. Typical values include formula, molecular weight, monoisotopic mass, ring count, Rule-of-Five status, and generated identifiers such as SMILES or InChI.

• Copy buttons next to identifiers let you move exact values into other tools quickly.
• When you work with a reaction, the overview follows the selected participant instead of staying fixed on the full reaction.
• Hide the Overview Sidebar when you want a larger canvas. A separate participant area remains available for reactions. Values marked Unavailable could not be calculated; they are not zero.

Export and share

Use File > Export... when you want to write the current molecule or reaction into another chemistry format. Use File > Share when you want to send the current molecule or whole reaction depiction as SVG, PNG, or PDF through standard macOS share destinations.

• Common molecule export choices include .svg depictions plus chemistry formats such as .sdf, .smi, .inchi, .mol2, .cml, and .rgf when R-group data can be written.
• ChemDraw CDX and ChemDraw CDXML export editable 2D molecules and reactions. Unsupported chemistry produces an error. Both formats can also be opened or imported into the Managed Repository. Unsupported chemistry produces an error; the original drawing is retained during repository import.
• Reaction documents can be exported as .rxn, .rdf, .rsmi, .rinchi, or reaction-bearing .cml.
• Save to Managed Repository... creates a managed repository entry instead of a general-purpose export.
• The repository save flow is intentionally narrower than Export: it accepts only chemistry file formats that AtomLens can reopen directly in a molecule or reaction window.

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