Sometime back I described how I was porting the VFLib algorithms to Java, so that we could use it for substructure search, since the current UniversalIsomorphismTester is pretty slow for this task, in general. While I had translated the Ullman algorithm implementation of VFLib and shown that it outperformed the CDK method, it turned out […]
Faster Substructure Search in the CDK
The CDK uses the UniversalIsomorphismTester to perform graph and subgraph isomorphism. However it’s not very efficient and this shows when performing substructure searches over large collections. A quick test where I compared the CDK code to OpenBabel’s obgrep showed that the CDK is nearly forty times slower than OpenBabel. Improvements in this code will enhance […]