Changes in version 1.0.0: NEW FEATURES o The eiR packages introduces efficient methods for accelerating structure similarity searches and clustering of very large compound datasets. The acceleration is achieved by applying embedding and indexing techniques to represent chemical compounds in a high-dimensional Euclidean space and to employ ultra-fast pre-screening of the compound dataset using the LSH-assisted nearest neighbor search in the embedding space. This method can drastically reduce the search time of large databases, by a factor of 40–200 fold when searching for the 100 closest compounds to a query.