Hi Tim,

I was looking through the new canon.cpp code, and it looks like a huge 
improvement over the original, and the tests we've been running are confirming 
this.  This is a big step forward.

But I noticed a rather alarming lack of comments in the new code.  There are 
some unfinished general comments towards the end of the file, but the various 
data structs and methods aren't explained, and I couldn't find anything about 
the overall algorithms you've implemented.

The reason this came up was because of the "c1(ccccc1)O" or "ugly SMILES" bug.  
I was hoping to be able to look at your new code and make some suggestions, but 
after an hour or two of scratching my head I was still lost.  I hope you'll 
have some time to write down all of the knowledge you put into the new 
canon.cpp code.

Thanks,
Craig

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