> Basically this means there is no clear resolution to the issue of  
> smi23d and patents.
...
> Sheesh, and all we did was implement an algorithm from a paper :(

Yes, I know the feeling. This is why so many people are against  
software patents. Of course the situation is not much better in wet  
chemistry -- someone can patent a process and then publish it. You  
can certainly repeat the published procedure, but the end result is  
still covered by patent. (Thus the problem with generic drugs and  
patents.)

I think Noel's discovery of RD-Kit and their 3D coordinate generation  
may make this point moot.

Similarly, I'm glad to finish the ring template database, since those  
can be used independently of any patent questions.

We'll get there -- and who knows, maybe they will clear the patent  
for open source use. It shouldn't affect the commercial side of their  
patent.

Cheers,
-Geoff


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