I’ve put released an update to rcdk and rcdklibs on CRAN – right now source packages are available, but binary ones should show up soon. Both packages should be updated together. These packages integrate the CDK into the R environment and simplifies a number of cheminformatics tasks. These versions used CDK 1.3.6 and JCP 16, so we now get access to SMSD and a few new descriptors.. In addition a some new methods have been included

• cdk.version to get the version of the CDK being used by the package
• is.subgraph uses SMSD to identify substructures. Similar to the pre-exisiting matches method, but much faster in general (though you cannot specify SMARTS)
• get.mcs again, wraps SMSD and allows one to retrieve the MCS (as a molecule object or as atom indices) for a pair of molecules. Once again, should be pretty fast