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 was previously done in a few steps. It involved
a BasicSceneGenerator, a BasicAtomGenerator, and a
BasicBondGenerator.
Nowadays, we can use the convenience class DepictionGenerator.
The code example looks like this:
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.
Figure 16.1: 2D diagram of triazole
Background color
Starting from the above pattern, you can also customize the background color.
This code uses the withParam() method to customize the rendering:
Script code/BackgroundColor.groovy
new DepictionGenerator()
.withSize(600, 600)
.withMargin(0.1)
.withZoom(3.0)
.withAtomColors()
.withParam(BasicSceneGenerator.BackgroundColor.class, Color.lightGray)
.depict(triazole)
.writeTo("BackgroundColor.png");
The result of this code is depicted in Figure 16.2.
Figure 16.2: Triazole depicted with a custom, grey background.
Parameters
Rendering wasn’t as much fun, if you could not tune it to your needs. JChemPaint has long had many rendering parameters, which are now all converting to the new API. The following code is an modification of the code example in snippet \ref{script:RenderMolecule}, and adds some code to list all rendering parameters for the three used generators:
Script code/RendererParameters.groovy
// generators make the image elements
List<IGenerator> generators =
new ArrayList<IGenerator>();
generators.add(new BasicSceneGenerator());
generators.add(new BasicBondGenerator());
generators.add(new BasicAtomGenerator());
// dump all parameters
for (generator in renderer.generators) {
for (parameter in generator.parameters) {
println "parameter: " +
parameter.class.name.substring(40) +
" -> " +
parameter.value;
}
}
The output will look something like:
parameter: BasicSceneGenerator$BackgroundColor -> java.awt.Color[r=255,g=255,b...
=255]
parameter: BasicSceneGenerator$ForegroundColor -> java.awt.Color[r=0,g=0,b=0]
parameter: BasicSceneGenerator$Margin -> 10.0
parameter: BasicSceneGenerator$UseAntiAliasing -> true
parameter: BasicSceneGenerator$UsedFontStyle -> NORMAL
parameter: BasicSceneGenerator$FontName -> Arial
parameter: BasicSceneGenerator$ZoomFactor -> 1.0
parameter: BasicSceneGenerator$Scale -> 1.0
parameter: BasicSceneGenerator$BondLength -> 40.0
parameter: BasicSceneGenerator$FitToScreen -> false
parameter: BasicSceneGenerator$ShowMoleculeTitle -> false
parameter: BasicSceneGenerator$ShowTooltip -> false
parameter: BasicSceneGenerator$ArrowHeadWidth -> 10.0
parameter: BasicSceneGenerator$ShowReactionTitle -> false
parameter: BasicBondGenerator$BondWidth -> 1.0
parameter: BasicBondGenerator$DefaultBondColor -> java.awt.Color[r=0,g=0,b=0]
parameter: BasicBondGenerator$WedgeWidth -> 2.0
parameter: BasicBondGenerator$BondDistance -> 2.0
parameter: BasicBondGenerator$TowardsRingCenterProportion -> 0.15
parameter: BasicAtomGenerator$AtomColor -> java.awt.Color[r=0,g=0,b=0]
parameter: BasicAtomGenerator$AtomColorer -> org.openscience.cdk.renderer.colo...
r.CDK2DAtomColors@35554635
parameter: BasicAtomGenerator$AtomRadius -> 8.0
parameter: BasicAtomGenerator$ColorByType -> true
parameter: BasicAtomGenerator$CompactShape -> SQUARE
parameter: BasicAtomGenerator$CompactAtom -> false
parameter: BasicAtomGenerator$KekuleStructure -> false
parameter: BasicAtomGenerator$ShowEndCarbons -> false
parameter: BasicAtomGenerator$ShowExplicitHydrogens -> true
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)