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.

When you have a ChemSpider (actually, RSC) account, go to your ChemSpider profile page. The API key is listed under the "Security Token" field. Copy that, and assign the string to $ChemSpiderAPIToken, which should look like this:

$ChemSpiderAPIToken = "ef739634-61c8-3c6c-6ff5-6d3a8a12f5d1"

(not my actual API key!)

You might wish to edit the notebook or the package itself so that $ChemSpiderAPIToken is permanently assigned to your API key.

I'll need to think of an easier way to let people enter their API keys.

I agree with your assessment; I have been using it for a while (and its predecessor functions for a while more), so I do have blind spots with respect to usability. (Feedback like yours is a good thing!)

I believe I did something like that for $ChemSpiderAPIToken in one of the initialization cells for molviewer.nb, but did not add one for gallery.nb. I'll commit that, along with fixes for some bug reports that have been sent in, in my next point (i.e., 1.1) release.

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.

@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.

As a passer by to this article I have to ask: why is a chemical "stick modeler" needed - albeit free?

Why I ask: Mathematica has chemical modeling built-in and also downloadable data (ie, molecules), including new extension to show electron affinity of bonds in a cloud/bond manner (and i think even keeping bond angles right). And I imagine Mathematica store has one or a few extenders of that. (i know only a little about Organic and Inorganic chemistry IUPAC naming and other things - i'm no chemistry professor though)

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.

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.