In order to accelerate the fragment search, we prepared an index file, which stores only the canonical SMILES of fragments and the corresponding position in fragment geometry database. When a match occurs, the file offset of the query fragment is retrieved and the database can be read directly to that position without requiring parsing or searching the entire database. While the latter is currently only ∼744 kb in size, as indicated in Table the use of this "table of contents" file improves performance by a factor of 2.6× (i.e., 140.9 s without the index to 54.8 s with the index).