The most popular similarity measure for comparing chemical structures represented by means of fingerprints is the Tanimoto (or Jaccard) coefficient T.
The Jaccard index, also known as the Jaccard similarity coefficient (originally coined coefficient de communauté by Paul Jaccard), is a statistic used for comparing the similarity and diversity of sample sets.
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In that paper, a "similarity ratio" is given over bitmaps, where each bit of a fixed-size array represents the presence or absence of a characteristic in the plant being modelled.
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