During the process of atmospheric nucleation, harmful substances may be generated, thus, it is with significant to conduct research on the process. In our previous work, some tools for visualization have already been developed. However, while the data set becomes larger, the computing time also increases accordingly. To make things worse, sometimes the visualization tool may become unstable due to some limitations, especially while calculating the similarity between molecules. In this paper, we will first propose an algorithm for calculating the similarity between two molecules. Then, in order to accelerate the parsing of data, the proposed algorithm will be implemented with parallel methods, and experimental results will show the improvement of the computing speed.
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