SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This enables us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure).
Kindly support the SMSD by citing the following publication :
S. Asad Rahman, M. Bashton, G. L. Holliday, R. Schrader and J. M. Thornton: Small Molecule Subgraph Detector (SMSD) Toolkit, Journal of Cheminformatics 2009, 1:12 doi:10.1186/1758-2946-1-12
Note: BUILD on Java 1.7