Version 3.0 of MoleculeViewer has just been released. Altho version 12 now has MoleculePlot3D[], the method for depicting multiple bonds in MoleculeViewer[] is markedly different. (The package also remains useful for older versions without built-in Molecule[] objects.) Using one of the examples in the docs for MoleculePlot3D[]:

MoleculeViewer["Nc1nccc(n1)c1c(C)onc1c1ccccc1"]

MoleculeViewer["Nc1nccc(n1)c1c(C)onc1c1ccccc1", PlotStyle -> "Tubes"]

Apart from the new multiple bond depiction style and the facility to change the depiction style for molecules (ball and stick, spacefilling, etc.), other features that have been added include

• data access functions for PDB and ZINC
• OCR for molecules using Imago OCR
• support for chemical structure drawing with Accelrys JDraw and JChemPaint
• ChEMBL Beaker support functions
• additional molecule manipulation functions

and many more.

m1 = ChEMBLSMILESTo3D["Nc1nccc(n1)c1c(C)onc1c1ccccc1", Method -> "ETKDG"];
bond = Reverse[Extract[Pick[##, "Single"] & @@ ArrayPad[m1, -1], 4]];
Animate[MoleculeViewer[BondRotate[m1, bond, ?],
                       PlotRange -> 600, ViewPoint -> {-0.832, 0.453, 3.265}],
        {?, 0, 2 ?, ?/12}]

Download the paclet from GitHub.

MoleculeViewer has been updated to version 1.1. Some updates include

• user is now explicitly prompted for a ChemSpider API key
• implemented detailed option settings for RunOpenBabel
• some minor tweaks and bug fixes

Please obtain the updated paclet from the GitHub releases page.

Why I ask: Mathematica has chemical modeling built-in and also downloadable data (ie, molecules)

• Right, this augments the built-in functionality. I've already noted the bit about depicting multiple bonds (which the default renderer does not do) in the very first post. Additionally, I do use ChemicalData[] as one possible source of info, but it does not have everything. (Try looking up the first and last examples in ChemicalData[] yourself and report back.)

And I imagine Mathematica store has one or a few extenders of that.

• If indeed there are, they did not show up in my searching efforts. Feel free to post links to anything you've seen. ;)

P. S. I am a chemist, FWIW.

@Murray Eisenberg, try opening Mathematica from the command line to have access to your usual $PATH. For me, I enter in the terminal

/Applications/Mathematica-11.2.app/Contents/MacOS/Mathematica &

and in the front end that pops up, you should see a different return for Environment["PATH"].

@J. M. - very cool visualizations!

I installed the MoleculeViewer paclet in the usual way, as well as openbabel (Macports version). And I registered with ChemSpider (which was a confusing procedure, as it involves first getting a Royal Society of Chemistry login and then linking tht with ChemSpider).

But how do I actually get that ChemSpider API key? And how do I tell MoleculeViewer about it?

I ask because when I tried to reevaluate a cell in the notebook gallery.nb, I got error message:

GetChemSpider: ChemSpider API key in $ChemSpiderAPIToken not detected or invalid

In order to use MoleculeViewer using Mathematica on macOS: which installation procedure will work with it for Open Babel?

• Macports?
• Conda (conda install open babel)?
• compile the source code (which is always a hassle).?

I'll try the MacPorts version of MoleculeViewer, as it seems to be the current version, as contrasted with the installer to which you supplied a link.

Homebrew is not a viable option on a Mac where one is already using MacPorts: using both can cause considerable confusion and clashes between different versions of libraries.