MoleculeViewer is a Mathematica package that renders molecules in a manner resembling physical molecular models. In particular, multiple bonds are depicted as out-of-plane bonds.
The package supports additional features like stylized molecule depictions (ball-and-stick, spacefilling, etc.), multiple atom legends, custom coloring of atoms, atom highlighting and tooltips.
The package also provides a number of auxiliary functions that use the services of Open Babel, Imago OCR, JME, Accelrys JDraw, JChemPaint, ChEMBL Beaker, ChemSpider, NCI CACTUS, PubChem, RCSB PDB, and ZINC.
Download the paclet from the releases page, and install it by evaluating the following in Mathematica:
Needs["PacletManager`"]
PacletInstall["/path/to/paclet/MoleculeViewer-1.0.paclet"]
where "/path/to/paclet/MoleculeViewer-1.0.paclet" should be replaced with the actual path to the downloaded paclet file.
See the file molviewer.nb for more detailed information on the package. A molecule gallery gallery.nb is also provided.