Athanor by arbastro
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The .athanor file format

Choose File › Download as .athanor. The file is a ZIP container holding a mimetype, document.json, one MOL V3000 file per structure under structures/, and a thumbnail. Unzip it to recover every structure without Athanor.

On a Mac, Ctrl is Cmd.

Save a document as a file

Choose Main menu › File › Download as .athanor. The file is named after the document, for example Aspirin.athanor. Your work is also kept automatically; this file is a copy you can keep, send or back up.

What is inside

An .athanor file is a ZIP container. A document with aspirin and caffeine on its page holds:

mimetype                 application/vnd.arbastro.athanor
document.json            the page: name, drawing standard, styling and the list of structures
structures/0001.mol      aspirin, as a MOL V3000 file
structures/0002.mol      caffeine, as a MOL V3000 file
thumbnail.png            a picture of the page
  • Every structure is a standard MOL V3000 file, so any chemistry program can read it. Rename the file to .zip, or open it with any unzip tool, to get them out without Athanor.
  • document.json carries what MOL files cannot: the document's name, its drawing standard (such as acs), and the page's styling, labels, groups and annotations. It has a version number, and newer versions of Athanor keep opening older files.

To open an .athanor file again, press Ctrl+O. See How to open structure files.

Files and formatsSupported file formatsExport (Ctrl+Shift+E) writes images (PNG, SVG, PDF, TIFF, EMF, EPS, JPEG, WMF), ChemDraw CDXML and CDX, chemistry files (MOL, SDF, SMILES, InChI, InChIKey, CML, Marvin, RXN, RDF) and computation files (XYZ, PDB, MOL2, Gaussian, ORCA).Files and formatsHow to open structure filesPress Ctrl+O (File › Open a file) and pick the file. An SDF with three compounds puts all three on the page, each named from the file.

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Last updated Nov 12, 2026