The IUPAC Chemical Identifier (InChI) is such a standardized identifier for chemical structures.
The Bioclipse project maintains OSGi bundles for InChI, making it easily available in any software application supporting the OSGi module system. It wraps the jni-inchi in OSGi bundles and publishes them on a p2 site.
The P2 site for the jni-inchi OSGi bundels is: http://pele.farmbio.uu.se/bioclipse/jni-inchi/
