osra

optical structure recognition
  https://sourceforge.net/p/osra/wiki/Home/
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OSRA is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES (Simplified Molecular Input Line Entry Specification) - a computer recognizable molecular structure format. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES representation of the molecular structure images encountered within that document.