Chemistry and Linux

If you are a) tired silly of both Microsoft's and Apple's attitudes b) ready to embrace, or already embraced Linux c) but still in need to prepare documents with embedded chemical structures, welcome to the club. Below are some tips on how to make it happen in Linux.

• Option 1: Still run Windows software

Use the same classic Microsoft Office/ChemDraw combo under Windows (not an) emulator, a.k.a. Wine. At least some versions of Microsoft Office (Word 2007, for instance), as well as ChemDraw (e.g. Ultra 8.0) work well under Wine. Unfortunatly, OLE embedding seems to be broken, which means you can't just double-click on your drawing, as normal, to edit it. You'll need to keep your original .CDX ChemDraw file, and copy/paste from it each time you need to make a change, just like the poor Mac people.

There are some attempts to have MacOS version of the software running as well (e.g. "Darling"), but I don't think they're quite there yet.

• Option 2: Substite with Linux software

MS Office equivalent: LibreOffice, or its long lost brother, Open Office, are available free for Linux. They substitute reasonably well for MS Office (Writer for Word, Impress for Powerpoint), are similar enough in capabilities, slightly different in arrangement, compatible for the most part.

ChemDraw equivalent: Does not quite exist. A number of structure drawing programs for Linux are out there (GChemPaint, BKChem, XDrawChem, JChemPaint, etc.), all have issues. I made the most use of BKChem, despite it being quite cumbersome. It is even possible to arrange in-place editing of drawings with it, like with ChemDraw under Windows. To do that:

• Download this macro.
• Go to Tools>Macros>Organize Macros>LibreOffice Basic, select "My Macros" and click "New" button. Copy and paste the content of the above file into the new macro, and save.
• Go to Tools>Customize, and link a keyboard shortcut (e.g. Ctrl-Alt-E) to lauch the macro "EditStructure", which should be under LibreOffice macros>user>Standard>Module1.
• Create a drawing in BKChem, save it (make sure to check "Auto crop image in SVG?" in File>File Properties dialog before saving).
• In LibreOffice, insert it via "Insert>Image>From file" menu.
• When you want to edit it, select it, and invoke the macro (via the keyboard the shortcut, e.g. Ctrl-Alt-E). That would open BkChem with your drawing.
• Edit, save it, and quit BKChem. Return to LibreOffice and click "OK" in the "Update drawing" dialog (or "Cancel" if you don't want to)

Hardcore Linux way: LibreOffice + LaTex.

• Install LibreOffice.
• Install LaTex. It needs to have "chemfig" package, which is often included in the distributon.
• Add TexMaths extention to LibreOffice.
• Click on π in TexMaths toolbar to add/edit a LaTex figure. Don't forget to include "\usepackage{chemfig}" in its Preamble.
• "Draw" structures by typing in instructions like "\chemfig{H-O-H}". See chemfig manual for details.
• P.S. If you want to go down that rabbit hole, there are other packages with different syntax: ochem, streetex, xymtex.