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!

The path thing seems to be an issue that is worth a separate question. It is indeed mystifying how path settings are inherited on the Mac.

In the meantime, for the upcoming point release (should be out by the coming weekend), I've now implemented a user dialog prompting a first-time user to enter his or her ChemSpider API key, which is then stored for subsequent sessions. This is hopefully less annoying than finding out from an error message that you had not entered the key yet.

Interesting, I thought the installer should have taken care of appending to the path environment variable. (It does on *nix and Windows, so Mac feedback is valuable!)

There is a procedure given here (alternatively, here), which as I see now is quite similar to what one does on *nix for editing PATH: go through the command line, and edit the PATH variable yourself with a text editor. (I am told one might sometimes need to reboot the computer after making such a change. In Ubuntu, I didn't have to.)

After all this, evaluate

Environment["PATH"]

in Mathematica to verify if the changes to PATH were saved, before loading the package.

Yes, definitely worth at least documenting what you just said about entering the ChemSpider API ID!

When others use a package, it's a wholly different thing when you, the package creator, uses it for himself (as I know all two well from my designing packages for students over many years). I urge some documentation in the standard Wolfram Documentation Center format for an add-on, so that it will be available when the use clicks the package name in the Documentation Center's Addons link.

And certain it would help now if you added to each of gallery.nb and movieviewer.nb a line

 $ChemSpiderAPIToken = "" (* enter your ChemSpider API ID here *)

with an explanatory text cell on how to retrieve it that ID.

Thank you for the package and your help in how to use it!

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.