Igor V. Filippov and Marc C. Nicklaus. Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution. J. Chem. Inf. Model. 2009, In press.
Unlike all existing software, OSRA is open source. You can get it right now from its web site.
One interesting point raised in the paper is how best to assess performance. It appears that a Tanimoto type fingerprint is highly penalised if even a single error is made. This is because an error such as replacement of an O with a C, although visually minor and easily corrected in a drawing package, is highly significant chemically. Perhaps a simple count of (bonds in common)/(union of bonds) would suffice although this would require mapping of bonds from the original structure to the recognised structure (the new SMSD tool by Syed Asad Rahman from Janet Thornton's group might help here).