Figure 5. System design of interactive visualization in GridMol.
The processes associated with rapid visualization and updating of changes made to 3D molecules, as well as how to ensure frequent data acquisition and avoid additional system burden, represent important fields of research. For molecular visualization, we used the scene graph, which is separated from the molecular structure and provides common characteristics, such as background, appearance, and molecule behavior, whereas the molecular structure uses atoms and bonds to allow zooming in/out and translation. This separation eliminates the need to repaint the total molecule and change the scene graph by simply translating atoms and redrawing the bonds, thereby significantly improving display efficiency.
To ensure frequent data acquisition, we set the data acquisition time interval to 10 seconds based on experimental analyses. Figure 6 illustrates the rule of incremental data-transfer from the breakpoint. During every data-checking activity, useful data are saved locally and a breakpoint established. When users check the calculation process, data are downloaded from only the breakpoint, thereby greatly reducing the burden on the grid and improving real time system performance.