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Molkit

Batch Export

Batch Export re-exports the named selections in a document in one step, one file per selection. Use it when a document holds many molecules that you export individually, for example a set of figures for a course, and you want to refresh all of them after a change.

Before you start

Batch Export works on named selections. A selection gets a name when you name it in the Named Selections panel, or when you type a name in the Filename field of the SVG, PNG, or PDF export dialog and export. Each named selection also remembers the options you last used to export it as SVG and as PNG.

If the document has no named selections, the dialog says so and the Export button is disabled.

Running a batch export

  1. Choose File > Batch Export….
  2. Under Format, pick SVG, PNG, or Both.
  3. Under Selections, clear the check box of any selection you do not want. Select none and Select all toggle the whole list. Each row shows the number of atoms (a) and, if any, annotations (n) in the selection.
  4. Under Destination, click Choose folder… to write the files into a folder. If you do not choose one, or your browser cannot write to folders (Firefox and Zen), Molkit downloads a single file named batch-export.zip. A folder you choose is offered again the next time you open the dialog, until you reload the page.
  5. Optionally set overrides (see below).
  6. Click Export. A status line shows progress, and a message reports how many files were written and any errors.

Files take the web-safe form of the selection’s name, so acetic acid becomes acetic-acid.svg, and a second selection with the same name gets -2. When the batch finishes, your selection on the canvas is restored as it was.

Warnings in the list

  • ⚠ edited: the molecule was changed after it was named, for example atoms were added or deleted. The export uses the saved members, which may no longer be the whole molecule.
  • ⚠ empty: nothing in the selection remains. The row cannot be checked.

Options for each file

By default, each selection is exported with the options it was last exported with in that format. A selection that has never been exported in that format uses these defaults:

  • SVG: scale 2, padding 20, no background, responsive, theme-aware, and mobile-safe, with fonts not embedded, labels kept as text, and no editable source.
  • PNG: scale 2, padding 20, no background.

SVG files always include the chemistry data and 3D geometry, as in a single SVG export. The editable copy of the drawing is included only when the selection was last exported with Include editable source or you turn on the Editable source override.

Overrides

Override for all (optional) changes an option for every file in this run. Each on/off option has three choices: Per-export (use each selection’s own setting), On for all, and Off for all. Scale and Padding offer Per-export or Set: with a value.

For SVG the on/off options are Background, Responsive, Theme-aware, Embed fonts, Mobile-safe fonts, Outline text, Maximum compatibility, Blank implicit H, and Editable source. For PNG the only on/off option is Background. With Both, the SVG and PNG overrides are kept separately; switch the format to set each.

Maximum compatibility works as in the SVG dialog: when it is on for a file, labels are outlined, theme-aware is off, and fonts are not embedded.

Check Remember these overrides as defaults for the exported selections to store the options used in this run on each exported selection, so later exports of those selections start from them.

See also