cdkbook
Depiction
The CDK originates from the merger of Jmol and JChemPaint [1]. As such, CDK has long contained code to depict molecules. However, after the 1.0 series, a rewrite of the code base was initiated, causing the CDK 1.2 series to not be available with rendering functionality. During the development of the 1.4 series, the rendering code became gradually available as a set of patches, and, separately, as a JChemPaint applet. The new rendering code has entered the CDK.
However, if you need rendering of reaction schemes or the editing functionality found in JChemPaint, you still need the CDK-JChemPaint patch.
Molecules
Rendering molecules to an image is done in a few steps. First, an Image needs
to be defined, for example, of 200 by 200 pixels. The next step is to define what is to be
generated, and how. The most basic rendering requires a few generators: one for the overall
scene, one for atoms, and one for bonds. Therefore, we add a BasicSceneGenerator,
a BasicAtomGenerator, and a BasicBondGenerator.
We will see later that we can add further generators to add further visualization.
Now that we defined what we want to have depicted, we construct a renderer. Because we
are rendering a molecule here, we simply use the AtomContainerRenderer.
Figure 16.1: 2D diagram of triazole
We also need to define, however, what rendering platform we want to use. The Java
community has a few options, with the AWT/Swing platform to be the reference implementation
provided by Oracle, and the SWT toolkit as a popular second. In fact, the redesign
was needed to be able to support both widget toolkits. For rendering images,
we can use the AWT toolkit. Therefore, we use a AWTFontManager to help the
renderer draw texts. We get our Graphics2D object to which will be drawn from the
earlier created image, and we set some basic properties.
Then we are ready to draw the molecule to the graphics object with the paint()
method, and here again we need a AWT-specific class: the AWTDrawVisitor.
What then remains is to save the image to a PNG image file with the
ImageIO helper class.
The full code example then looks like:
Script code/RenderMolecule.groovy
new DepictionGenerator()
.withSize(600, 600)
.withMargin(0.1)
.withZoom(3.0)
.withAtomColors()
.depict(triazole)
.writeTo("RenderMolecule.png");
This results in the image of triazole given in Figure 16.1.
Background color
Starting from the common pattern to set up a renderer used in the earlier sections,
you can also customize the background color. This too uses a parameter, but the
color is also passed to the Graphics2D object:
Script code/BackgroundColor.groovy
backgroundColor = Color.lightGray;
model = renderer.getRenderer2DModel()
model.set(
BasicSceneGenerator.BackgroundColor.class,
backgroundColor
)
// paint the background
Graphics2D g2 = (Graphics2D)image.getGraphics();
g2.setColor(backgroundColor);
g2.fillRect(0, 0, WIDTH, HEIGHT);
The result of this code is depicted in Figure 16.2.
Figure 16.2: Triazole depicted with a custom, grey background.
References
- Krause S, Willighagen E, Steinbeck C. JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures. Molecules. 2000 Jan 28;5(1):93–8. doi:10.3390/50100093 (Scholia)