The paper uses the rendering functionality of the CDK. The authors write:
- The viewer application uses code from the Chemistry Development Kit(31) (CDK) to display graphical representations of the compounds involved in the reactions. The CDK source code was altered to enable the color-coded display of the bonds that were broken or formed during the reaction as shown in Figure 7. In addition, we created a “transition state” molecule that shows the transitory combination of reactant molecules that occurs at a potential energy maximum. The CDK source code was also modified to support the display of the transition state.
The source code is, as the title promises, open source, and available from the armsrc project on SourceForge.