I don't have a Mac, but it seems Conda or HomeBrew are recommended here. Alternatively, there is a link to an installer here. Let me know if you can get it to work!

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

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!

Next issue: how to tell RunOpenBabel the path on which to find the openbabel binary obabel. The program is in my macOS system path (at /opt/local/bin/obabel).

I ask because I tried in your notebook molviewer.nb to execute the code:

MoleculeViewer[RunOpenBabel[GetChemSpider["ixabepilone", "InChI"]], 
 PlotLegends -> True]

But that gave an error:

RunProcess: Program babel not found. Check Environment'"PATH"]

Although the location of babel is on my system path — which is set in ~/.profile — still Mathematica is not recognizing that:

    Environment["PATH"]
/usr/bin:bin:/usr/sbin:/sbin

and hence your RunOpenBabel function fails with the same error I listed. This is even after a system reboot.

The link you provide for changing the value of PATH will probably lead to chaos on macOS, because if the file .bash_profile exists, then .profile will not even be read by the shell, and .profile is where MacPorts and other apps place additions to PATH (along with various command aliases).

What's even stranger is the following. In a new Mathematica session, before loading MoleculeViewer, I evaluate the commands

    SetEnvironment["PATH" -> StringJoin[Environment["PATH"], ":opt/local/bin"]]
    Environment["PATH"]

and get output:

/usr/bin:/bin:/usr/sbin:/sbin:opt/local/bin

The last location there, /opt/local/bin is definitely where the obabel executable resides, as I can check with the Mac's system command:

mdfind -name obabel

And indeed, in a Terminal session I can evaluate, e.g., either of:

obabel -H
/opt/local/bin/obabel -H

and get the expected output.

But why is Mathematica not picking up the path from /etc/paths (really /private/etc/paths) and /etc/paths.d (really, /private/etc/paths.d) files?

As I indicated in a previous reply, one of the paths in /etc/paths is not being picked up by Mathematica as shown in the output from evaluating Environment["PATH"].

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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.

Version 2.0 of MoleculeViewer has been released. The package now uses the new API system for ChemSpider, so users of previous versions will need to register for a new API key on the RSC page.

Additionally, the PubChem API is now also used to obtain structural information. For example:

MoleculeViewer[GetPubChem["fexofenadine"]]

Support for files and URLs has also been implemented:

MoleculeViewer["http://exampledata.wolfram.com/aspirin.mol"]

as well as chemical Entity[] objects:

Download the paclet from GitHub.