A new paper has been published that describes the module used to process chemical components in deposited PDB entries as part of the new wwPDB Common Deposition and Annotation System:
J.Y. Young, Z. Feng, D. Dimitropoulos, R. Sala, J. Westbrook, M. Zhuravleva, C. Shao, M. Quesada, E. Peisach, H.M. Berman. (2013) Chemical annotation of small and peptide-like molecules at the Protein Data Bank. Database 2013: bat079.
This new system is currently in testing. For more information, see wwpdb.org.