Obscure Essentials™ by Sascha Losko

Work With Structure Documents

The main AtomLens document window is where you paste, render, inspect, and export a molecule or reaction context.

Workspace areas

The document window is organized around an input sidebar on the left, an interactive drawing canvas in the center, and the Overview sidebar on the right. Use the toolbar to show or hide sidebars, adjust depiction style, and switch reaction-specific drawing options when they apply.

On this page

Opening documents

You can open chemistry files from Finder, from File > Open... , from Open Recent , or from the Molecule 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, Browse opens the Managed Repository.
  • 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

The input sidebar accepts pasted or typed chemistry text. AtomLens detects the current input format when possible and enables Parse & Render once the text is usable.

  • Clear removes the current input, drawing, and computed identifiers.
  • Enter an IUPAC name... opens a name dialog, converts supported names to CML, and renders the result directly.
  • Parse & Render rebuilds the depicted structure from the current input.
  • The sidebar is especially useful when you need to review a SMILES, InChI, or reaction string quickly without first creating a file.

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.
  • 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.

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.
  • Both sidebars can be hidden if you want a larger canvas.

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.
  • 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.
Next step: If you want to explore arbitrary Mac files before opening them, continue to Browse Local Files . If you want AtomLens-managed storage that is available on Mac and iPad, continue to Managed Repository and iCloud sync .