On Apr 11, 2013, at 1:39 PM, Quentin Delettre wrote:
> I was more concerned about algorithms/implementation, pitfalls that
> could happen and performance.
There are none. "Pretty much every cheminformatics toolkit can do
what you want."
The toolkits I know of use either the Ullmann algorithm or the VF2
algorithm. Most use VF2, and that transition occurred some 5 years ago.
There are toolkit variations. In one benchmark I measured a factor of 5x
between RDKit and OEChem. There are also special cases where one toolkit
might be a lot better than another; Roger Sayle pointed out that there's
a huge variation for matching the radioactive isotopes.
However, those won't be a problem in the scenario you described. You may
have to wait a few minutes longer for one toolkit than the other, but
RDKit does about 100,000 matches per second (for a simple match), so
could finish your task in less time then you've spent on this email
thread.
Cheers,
Andrew
da...@dalkescientific.com
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