Quick Start

Start with bundled examples, open a file, parse pasted chemistry text, inspect the structure, then save, share, or extract what you need.

Start with a file or pasted text

Start in Library. Open chooses a chemistry file from Files; New > Draw Structure or New > Enter Structure Source starts an isolated draft. The source editor also converts supported IUPAC names.

AtomLens automatically switches between molecule and reaction workflows based on the content you open.

• Import covers molecule formats such as MOL, SDF, SMILES, CXSMILES, InChI, MOL2, PDB, XYZ, CML, and RGfile, plus reaction formats such as Reaction SMILES, RInChI, RXN, RDF, and reaction CML.
• If you paste text instead of opening a file, AtomLens keeps the session editable so you can refine the input and parse again.

Start without your own files

AtomLens includes example structures and reactions so you can explore the iPad workflow even when you do not have chemistry files nearby.

On first launch, leave Add example structures and reactions selected on the Welcome screen and tap Continue. Later, open Settings, choose Managed Repository, and tap Add Example Structures and Reactions.

• The example set includes 20 ChEBI Entity of the Month structures and 20 Rhea-derived reactions.
• Examples are stored in the Managed Repository, using iCloud when repository sync is enabled and available.
• AtomLens compares structure InChIKeys and reaction long RInChIKeys during import, so importing the examples again skips entries that are already present.

Read the document workspace

The document workspace centers on the live canvas and the Overview Sidebar. Edit Structure Source or Edit Reaction Source opens a separate text editor; Draw Structure or Draw Reaction opens a separate drawing editor. There is no permanent input sidebar.

• Choose View > Overview to show or hide the details alongside the canvas.
• If a reaction is loaded, the overview sidebar follows the currently selected participant.

Finish the current task

Use Save when you want a single AtomLens-readable chemistry file stored in the Managed Repository. Use Share when you want the current depiction handed to the system share sheet as SVG, PNG, or PDF. Use Extract when the source contains multiple records and you want AtomLens to split or summarize them in one pass.

• Library is the home screen for your Managed Repository. The Library back button returns to the same search and filters. Open Documents resumes your open tabs; returning to Library does not close them.
• Use the reactions-only filter in Managed Repository when you want to focus on reaction records.
• Open Help from Library or More > Help in a document. Done returns to the screen you came from.