So much to do, so little time

Trying to squeeze sense out of chemical data

Archive for the ‘matching’ tag

Java Port of VFLib Works and it’s Blazing

with 8 comments

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 that didn’t work for certain cases such as finding CCC in C1CC1. This was due to a different definition of isomorphism that VFLib used. Instead, I tried to convert the VF2 implementation to Java. The motivation was that it does indeed perform substructure matching as is usually understood in cheminformatics, and was also reported to be extremely fast. Unfortunately, my translation was buggy and I put it on hold.

Read the rest of this entry »

Written by Rajarshi Guha

November 18th, 2008 at 11:17 pm