Chemistry on the Desktop

For this article, I thought I'd introduce another chemistry application—specifically, BKChem, a free chemical drawing program. As opposed to many other chemistry applications, BKChem provides both a nice GUI for constructing molecules and a set of chemical analysis tools to look at the properties of the newly constructed molecule.

Most distributions should have a package available to make installation easier—for example, Debian-based distributions can install BKChem with the following command:

sudo apt-get install bkchem

Once BKChem is installed, you can start it either from the menu entry or by executing the command bkchem from a terminal window.

When it first opens, you'll see a blank screen where you can start your chemical construction.

Figure 1. When you first start BKChem, you get a blank canvas to start building your molecule.

If you have a previously created molecule, you can load it by clicking the File→Load menu item, which will load the data into a new tab, or you can click the File→Load to the same tab menu option to load it into the currently active tab.

BKChem also can import data from other file formats. If you click File→Import, you'll see that you can import files with CML, CML2 or Molfile formats.

If you want to start by building your own molecule, several menus of building blocks are available. They are laid out as a pair of rows, just below the menu listings at the top of the window. The top row of icons selects which list of icons will be available in the second row. The first icon in the first row is simply an arrow, allowing you to select objects within your molecule so you can edit their properties. The next icon pulls up the row of drawing elements where you can start to draw your new molecule.

There are several choices in terms of line thicknesses, styles and bond angles, and you can create a chain of elements simply by clicking on the end of an existing line segment.

Once you have the basics of your structure laid out, you'll want to edit the details next. To do this, click on the first icon again (captioned with "edit"), and then click on the structure element you want to edit. This is where having a proper mouse is a must, as you need to click with the middle button on your mouse to pull up the edit panel.

Figure 2. You can edit an element by clicking the middle mouse button. The menu you get depends on the type of element you are editing.


Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.