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.